Integrated sample processing system with variable workflows

ABSTRACT

One embodiment of the invention is directed to a sample processing system for analyzing a biological sample from a patient. The sample processing system comprises: a plurality of analyzers comprising at least one mass spectrometer, wherein each analyzer in the plurality of analyzers is configured to acquire at least one measurement value corresponding to at least one characteristic of the biological sample; at least one data storage component which stores (i) a list of parameters for the plurality of analyzers, and (ii) at least two condition sets, which contain data associated with completing one or more test orders. The condition sets contain data which differ by at least one variable; and a control system operatively coupled to the plurality of analyzers, and the at least one data storage component. The control system is configured to (i) determine which condition set of the at least two condition sets to use based on the determined condition set, (ii) determine which analyzer or analyzers of the plurality of analyzers to use to process each test order based on the determined condition set and one or more parameters from the list of parameters, and (iii) cause the determined analyzer or analyzers to acquire one or more measurement values for the biological sample.

CROSS-REFERENCES TO RELATED APPLICATIONS

This application claims priority to U.S. Provisional Application No.62/607,685 filed on Dec. 19, 2017, the contents of which areincorporated by reference in their entirety for all purposes.

BACKGROUND

Mass Spectrometry (MS) is an analytical technique used for determiningthe elemental composition of samples, quantifying the mass of particlesand molecules, and elucidating the chemical structure of molecules.Various types of MS with high specificity, such as Liquid Chromatography(LC-MS), Gas Chromatography (GC-MS), and Matrix-Assisted LaserDesorption/Ionization/Time-Of-Flight (MALDI-TOF MS), are beingincreasingly used in clinical diagnostics. These MS techniques overcomemany of the limitations of immunoassays (e.g. non-specific binding andcross reactivity of analytes) and offer many advantages).

To date, MS techniques have not found widespread clinical applicationdue to challenges including sample preparation, online extraction,throughput, automation, laboratory information system interfacing,inter-instruments standardization and harmonization.

Further, the use of MS alone as a diagnostic tool has drawbacks. Forexample, MS is highly sensitive and can be more costly to run than othertypes of analyses. Further, because analytes need to be volatile in massspectrometry, the number of sample preparation steps can be greater thanother types of analyzers. Thus, MS may not be the optimal method foranalyzing all types of biological samples under every circumstance.

Embodiments of the invention address these and other challenges,individually and collectively.

BRIEF SUMMARY

Some embodiments of the invention may include an integrated sampleprocessing system that can include multiple analyzers, at least one ofwhich is a mass spectrometer. Embodiments of the invention may alsoinclude a control system, which can be used to select an analyzer orcombination of analyzers, one of which can be a mass spectrometer, toprocess a particular biological sample. The selection of which analyzeror combination of analyzers can depend upon a number of factorsincluding the characteristics of the particular biological sample, oneor more condition sets, analyzer parameters, and information in a testorder for the biological sample.

One embodiment of the invention is directed to a sample processingsystem for analyzing a biological sample from a patient, the sampleprocessing system comprising: a plurality of analyzers comprising atleast one mass spectrometer, wherein each analyzer in the plurality ofanalyzers is configured to acquire at least one measurement valuecorresponding to at least one characteristic of the biological sample;at least one data storage component which stores (i) a list ofparameters for the plurality of analyzers, and (ii) at least twocondition sets, which contain data associated with completing one ormore test orders, wherein the at least two of the condition sets containdata which differ by at least one variable; and a control systemoperatively coupled to the plurality of analyzers, and the at least onedata storage component, and wherein the control system comprises acomputer readable medium and a data processor. The computer readablemedium comprises code, executable by the processor to cause the controlsystem to (i) determine which condition set of the at least twocondition sets to use based on the determined condition set, (ii)determine which analyzer or analyzers of the plurality of analyzers touse to process the one or more test orders based on the determinedcondition set and one or more parameters from the list of parameters,and (iii) cause the determined analyzer or analyzers to acquire one ormore measurement values for the biological sample.

Another embodiment of the invention is directed to a method performed bya system comprising a plurality of analyzers comprising at least onemass spectrometer, at least one data storage component storing aplurality of condition sets, the condition sets in the plurality ofcondition sets differing by at least one variable, and a plurality ofparameter lists for the plurality of analyzers, and a control systemcoupled to the plurality of analyzers, and the at least one data storagecomponent. The method comprises determining, by the control system, inresponse to receipt of a test order to test a biological sample, one ormore condition sets of the plurality of condition sets in the datastorage component to use to complete the test order; determining, by thecontrol system, an analyzer or analyzers from the plurality of analyzersto use to process the biological sample based on the one or morecondition sets, and one or more parameters in the parameter lists in theplurality of parameter lists, the determined analyzer or analyzersincluding the at least one mass spectrometer, and causing, by thecontrol system, the determined analyzer or analyzers of the plurality ofanalyzers to process the biological sample to determine one or moremeasurement values for the biological sample.

These and other embodiments of the invention are described in furtherdetail below, with reference to the drawings.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1A shows a block diagram of an sample processing system accordingto an embodiment of the invention.

FIG. 1B shows a block diagram of a sample staging apparatus according toembodiment of the invention.

FIG. 1C shows a flowchart illustrating a method according to embodimentof the invention.

FIG. 2 shows a diagram illustrating different processing paths that canbe taken in the sample processing system according to embodiments of theinvention.

FIG. 3 shows a high level flowchart illustrating processing stepsperformed by a sample processing system according to embodiments of theinvention. The flowchart illustrates different detection operations thatcan be performed in the sample processing system.

FIG. 4A shows a diagram of an analyzer in a sample processing systemaccording to an embodiment of the invention.

FIG. 4B shows an illustrative flow chart diagram showing operatingprocedures for operating an analyzer.

FIG. 4C shows a perspective view showing an arrangement of a main samplepipetting station and a sample storage of the analyzer.

FIG. 5A shows a top/side cross-sectional view of an incubation carouselaccording to an embodiment of the invention.

FIG. 5B shows a top/side perspective and cross-sectional view of aportion of the incubation carousel in FIG. 5A.

FIG. 5C shows a top perspective view of a portion of the incubationcarousel in FIG. 5A.

FIG. 6A shows a block diagram of a mass spectrometer.

FIG. 6B shows a portion of a mass spectrometer using an electrospraymethod.

FIG. 6C shows a structure of an ion detector used in a massspectrometer.

FIG. 7A shows a diagram of trap and elute system according to anembodiment of the invention in a first configuration.

FIG. 7B shows a diagram of trap and elute system according to anembodiment of the invention in a second configuration.

FIG. 8 shows a flowchart illustrating an immunopurification processaccording to an embodiment of the invention.

FIG. 9 shows a flowchart illustrating a protein precipitation processaccording to an embodiment of the invention.

FIG. 10 shows a flowchart illustrating another immunopurificationprocess according to an embodiment of the invention.

DETAILED DESCRIPTION

Embodiments of the invention may be used to detect the presence,absence, or concentration of analytes in biological samples. Biologicalsamples such as biological fluids may include, but are not limited to,blood, plasma, serum, or other bodily fluids or excretions, such as butnot limited to saliva, urine, cerebrospinal fluid, lacrimal fluid,perspiration, gastrointestinal fluid, amniotic fluid, mucosal fluid,pleural fluid, sebaceous oil, exhaled breath, and the like.

The term “analyzer” may include any suitable instrument that is capableof analyzing a sample such as a biological sample. Examples of analyzersinclude mass spectrometers, immunoanalyzers, hematology analyzers,microbiology analyzers, and/or molecular biology analyzers.

The term “measurement value” may include a specific value that isobtained in relation to an analysis of a biological sample. Themeasurement value may be determined by the one or more analyzers, or byan information management apparatus that obtains data from one or moreanalyzers. For example, a specific measurement value associated with abiological sample being analyzed by a mass spectrometer might be aspecific mass to charge ratio that is observed for an analyte in thebiological sample. Other types of measurement values may includefluorescence values. Measurement values may be in the form of raw datafrom an analyzer, or may be in form of data that is derived from rawdata. In some cases, derived data can be more readily interpreted bysystem users than raw data. For example, fluorescent values from ananalyzer may be converted to different numerical values such asconcentration values. Either may be considered “measurement values.”

A “characteristic” of a biological sample may include a property of thebiological sample. The property of the sample may relate to thepresence, absence, or quantity of components (e.g., organisms, proteins,etc.) in the sample. Characteristics of biological samples may alsorelate to disease conditions that might or might not be associated withthe biological samples. For example, characteristics of biologicalsamples may include whether or not those biological samples areassociated with diseases such as Alzheimers, cardiac disease, breastcancer, colorectal cancer, prostate cancer, ovarian cancer, lung cancer,pancreatic cancer, bladder cancer, and heptatocellular cancer. Acharacteristic of the biological sample may also pertain to a physicalproperty of the biological sample, such as the color or appearance ofthe biological sample.

The term “parameter” may include a factor that relates to a condition ofoperation of an instrument such as an analyzer. Parameters may relate todetection ranges for different analyzers, types of measurement valuesobtainable by the analyzers, the costs of operating various analyzers,the availability (or scheduling) of analyzers, when calibrations werelast completed, availability of personnel to perform manual samplepreparation or operate analyzers; etc.

The term “condition set” may include one or more rules for handlingspecific types of biological samples. Each condition set may include aplurality of variables that may be associated with the one or morerules. Laboratory rules may include rules for handling samples,detection ranges needed to meet orders, etc. For example, a firstcondition set may include a first rule which states that if the patientis a female, then the patient's biological sample needs to be testedusing a mass spectrometer. A second condition set may include a secondrule that states if the patient is a male, then the patient's biologicalsample can be tested by using an immunoanalyzer or a mass spectrometer.Males generally have higher levels of testosterone than females, andthese higher levels of testosterone can be detected using animmunoanalyzer or a mass spectrometer. On the other hand, becausefemales have lower levels of testosterone, the lower levels oftestosterone may not be detectable using an immunoanalyzer, but may bedetectable by a mass spectrometer. In the latter case, a massspectrometer may be the appropriate analyzer to use to analyze thefemale's biological sample. In another example, a condition set mayspecify that a mass spectrometer is to be used if the test orderrequests testing for a protein marker (the expression of which maycorrelate to a disease), a steroid (e.g., testosterone, estradiol, orprogesterone), or for vitamin D. In yet other examples, condition setsmay be used to specify if retest or reflex processing is to occur and onwhich analyzers for a particular biological sample, upon certainpredetermined results from a primary analysis of the biological sample.Conditions sets could also be chosen based on the order; for example, ifa clinician specifies that the analyte be determined with MS versus IA.Conditions sets could also be chosen based on a particular clinician;for example, an order submitted by a OBGYN could automatically include apregnancy test.

The term “variable” may include a component of a rule in a condition setthat can vary. For example, if a condition set includes a rule thatstates that if the patient is a male, then the patient's biologicalsample can be tested by using an immunoanalyzer or a mass spectrometer,then the variables that can be present in this condition set can be thesex of the patient (e.g., “male”), and the type of analyzer used (e.g.,an “immunoanalyzer,” and/or a “mass spectrometer”). Variables maypertain to characteristics of the patient from which the biologicalsample was obtained (e.g., the age, sex, ethnicity, pre-existingconditions of a patient, insurance coverage status of the patient),characteristics of the specific type of analyzers, specific types ofanalyzers, time periods for processing (e.g., process now or later),sample types (e.g., blood, urine, etc.) etc. A variable may also bedetermined by a laboratory according to factors that may be independentof the specific characteristics of a biological sample. For example, alaboratory provide a predetermined value that may be a variable thatindicates a preference of analyzer use. This may be based upon thereliability or age of the analyzers.

The term “patient information” can include any suitable data related toa patient. Patient information may include, but is not limited to, atleast the following types of information: demographic information (name,address, phone), biometric information, patient ID information (uniqueidentifier used to tag samples), imaging information (x-ray, CT, MRI,US), surgical information, pharmaceutical information (e.g., specificdrugs a patient is taking or should take and in what dose), billinginformation, EMR information, physician generated information (e.g.,vital signs, observations, medical changes), and historical patientinformation (e.g., drug levels being monitored, chronic diseaseinformation, information about adverse drug reactions, etc.)

The term “test order” may include any suitable type of instruction forprocessing a biological sample. Exemplary test orders may includepatient information associated with biological samples, the health careproviders requesting the testing of the biological samples, tests to beperformed on the biological samples (e.g., the detection of the presenceor absence of specific analyte(s)), and the expected processing times(e.g., a STAT or short turnaround time sample) associated with thebiological samples. Test orders may also specify specific types ofanalyzers to use to analyze the biological sample.

The term “analyte” may include a substance whose presence, absence, orconcentration is to be determined according to embodiments of thepresent invention. Typical analytes may include, but are not limited toorganic molecules, hormones (such as thyroid hormones, estradiol,testosterone, progesterone, estrogen), metabolites (such as glucose orethanol), proteins, lipids, carbohydrates and sugars, steroids (such asVitamin D), peptides (such as procalcitonin), nucleic acid segments,biomarkers (pharmaceuticals such as antibiotics, benzodiazepine), drugs(such as immunosuppressant drugs, narcotics, opioids, etc.), moleculeswith a regulatory effect in enzymatic processes such as promoters,activators, inhibitors, or cofactors, microorganisms (such as viruses(including EBV, HPV, HIV, HCV, HBV, Influenza, Norovirus, Rotavirus,Adenovirus etc.), bacteria (H. pylori, Streptococcus, MRSA, C. diff.,Ligionella, etc.), fungus, parasites (plasmodium, etc.), cells, cellcomponents (such as cell membranes), spores, nucleic acids (such as DNAand RNA), etc. Embodiments of the invention can also allow for thesimultaneous analysis of multiple analytes in the same class ordifferent classes (e.g. simultaneous analysis of metabolites andproteins). In embodiments of the invention, the analysis of a particularanalyte such as a biomarker may indicate that a particular condition(e.g., disease) is associated with a sample that contains the analyte.

The term “immunoassay” can be a laboratory method used to determine theamount of an analyte in a sample. It can be based on the interaction ofantibodies with antigens, and because of the degree of selectivity forthe analyte (either antigen or antibody), an immunoassay can be used toquantitatively determine very low concentrations of analyte in a testsample. “Immunoanalyzer” can include an instrument on which immunoassayshave been automated. Various immunoanalyzers are commercially availableincluding the DxI™ system (Beckman Coulter, CA), the ADVIA™ and CENTAUR™systems (Siemens Healthcare, Germany), the COBAS™ system (RocheDiagnostic, Germany), the ARCHITECT™ system (Abbott, IL), the VITROS™system (Ortho-clinical Diagnostic, NJ), and the VIDAS™ system(Biomerieux, France).

The term “mass spectrometer” may relate to an instrument which canmeasure the mass-to-charge ratios and relative concentrations of atomsand molecules. One example of a mass spectrometer makes use of the basicmagnetic force on a moving charged particle. Basically, the instrumentionizes a sample and then deflects the ions through a magnetic fieldbased on the mass-to-charge ratio of the ion. The mass spectrum can thenbe used to determine the elemental or isotopic signature of a sample,the masses of particles and of molecules, and to elucidate the chemicalstructures of molecules, such as peptides and other chemical compounds.Commercially available mass spectrometers can be categorized based onhow they sector mass selection, including time-of-flight, quadrupole MS,ion traps (including 3D quadrupole, cylindrical ion traps, linearquadropole ion traps, orbitraps), fourier transform ion cyclotronresonance (FT-ICT), etc. Alternatively, they can be sectored based onion source (laser desorption, matrix assisted laser desorption, thermalionization, plasma, spark source, electrospray, etc.) or detectors(electron multipliers (such as Faraday cups and ion-to-photondetectors), inductive dectectors, etc.). In a preferred embodiment, themass spectrometer can be a triple quadrupole mass spectrometer.

One embodiment of the invention is directed to a method performed by asystem comprising a plurality of analyzers comprising at least one massspectrometer, and at least one data storage component. The plurality ofanalyzers may include multiple analyzers of the same type (e.g., atleast two mass spectrometers), or different analyzers (e.g., oneimmunoanalyzer, one mass spectrometer, one hematology analyzer, etc.).The data storage component stores a plurality of condition sets, thecondition sets in the plurality of condition sets differing by at leastone variable. The data storage component also stores parameter lists forthe plurality of analyzers. The system also includes a control systemcoupled to the plurality of analyzers, and the at least one data storagecomponent. The control system can perform a method comprisingdetermining in response to receipt of a test order to test a biologicalsample, one or more condition sets of the plurality of condition sets inthe data storage component to use to complete the test order. Once theone or more condition sets are determined, the control system determinesan analyzer or analyzers from the plurality of analyzers to use toprocess the biological sample based on the determined one or morecondition sets and one or more parameters. The one or more determinedanalyzer or analyzers include the at least one mass spectrometer. Themethod also includes causing, by the control system, the determinedanalyzer or analyzers of the plurality of analyzers to process thebiological sample to determine one or more measurement values for thebiological sample.

Embodiments of the invention can include an integrated platform with amass spectrometer (measuring mass) and one or more additional analyzers.In some embodiments, the mass spectrometer and the various analyzers canbe present within the same housing. In other embodiments, the at leastone mass spectrometer and the other analyzers can be in separatehousings. In some embodiments, the analyzer can be an immunoanalyzer(typically detecting a label (chemoluminescent, electrochemiluminescentfluorescent, radioactive, isotope, DNA, etc. or label free system).Other types of analyzers may include hematology analyzers, microbiologyanalyzers, chemistry analyzers, urine analyzers, biochemical analyzers,and/or a molecular biology analyzers. When analyzing a biologicalsample, one or more of these types of analyzers, in any suitablecombination, may be used to analyze the biological sample.

A hematology analyzer can be used to perform complete blood counts,erythrocyte sedimentation rates (ESRs), and/or coagulation tests.Automated cell counters sample the blood, and quantify, classify, anddescribe cell populations using both electrical and optical techniques.

A microbiology analyzer can function as a diagnostic tool fordetermining the identity of a biological organism. In some embodiments,a microbiology analyzer can identify an infecting microorganism. Suchanalyzers can use biochemicals in a plurality of small sample testmicrowells in centrifugal rotors that contain different substrates, orin multi-well panels, depending on the type of test being performed.

A molecular biology analyzer can be a device which can analyze abiological sample at its molecular level. An example of a molecularbiology analyzer may include a nucleic acid analyzer such as a DNAanalyzer.

A chemistry analyzer can run assays on clinical samples such as bloodserum, plasma, urine, and cerebrospinal fluid to detect the presence ofanalytes relating to disease or drugs. A chemistry analyzer may usephotometry. In photometry, a sample is mixed with the appropriatereagent to produce a reaction that results in a color. The concentrationof the analyte determines the strength of color produced. The photometershines light of the appropriate wavelength at the sample and measuresthe amount of light absorbed, which is directly correlated to theconcentration of the analyte in the sample. Another analytical methodused in a chemistry analyzer is the use of ion selective electrodes(ISE) to measure ions such as Na⁺, K⁺, Cl⁻, and Li⁺ An TSE is a sensorthat determines the concentration of ions in a solution by measuring thecurrent flow through an ion selective membrane.

Embodiments of the invention can include a system that uses two or moreanalyzers, one of which is a mass spectrometer. The analyzers may beused in any suitable combination to process biological samples. In someembodiments, a sample staging apparatus can also be present in thesystem. The sample staging apparatus may be used to present samples orportions of samples to the analyzers that are used to process thebiological sample.

The system also comprises a control system that can control the massspectrometer, the various analyzers, and the sample staging apparatus.The sample staging apparatus can be separate from or shared with any ofthe analyzers in the system. In some cases, the sample staging apparatusmay include a track or transport system that can transport or routesample containers or sample vessels within the system. The systemaccording to embodiments of the invention can be capable of (1)independent analysis by one or more analyzers and/or (2) serial orparallel analysis by one or more analyzers. Serial analysis can includeeither retesting (e.g., same analyte tested on both analyzers) or reflextesting (e.g., a first analyte is tested on one analyzer (typically theimmunoanalyzer) and a second or more analyte(s) are tested on the otheranalyzer (typically the mass spectrometer)).

In some cases, a single sample staging apparatus is used for all of theanalyzers (e.g., including the mass spectrometer). In other embodiments,sample preparation stations are present for each of the analyzers, and acommon sample staging apparatus is not needed in all embodiments. Eachsample preparation station comprises a means (or device) for aliquottingthe sample (such as an aliquottor), and means for holding at least onereagent pack comprising the reagents needed for the various analyzers.In some embodiments, the sample preparation station comprises a meansfor holding different reagent packs for the different types of analyzersin the system.

In some embodiments, the system may include a sample introduction systemthat allows for the direct transfer of a biological sample between twoanalyzers. The sample introduction system for introducing a sample toone or more of the analyzers can be fluidically linked to at least oneof the sample preparation systems in one of the other analyzers oroutside of the one or more analyzers. In some embodiments, the sampleintroduction system may include direct flow injection, the use of a trapand elute system (e.g., a trap and elute system which includes 2 pumpsand a 6-port switching valve), the use of an open port apparatus such asan open port probe.

The control system according to embodiments of the invention can performa number of additional functions. For example, the control system cancause the sample processing system to process a primary sample andprovide results regarding the presence, absence, or quantity of aparticular analyte in the primary sample. The control system can furthercause the sample processing system to process a second sample andprovide results regarding the presence, absence, or quantity of one ormore analytes in the second sample. The first and second samples can beprocessed by the same analyzer (e.g., an immunoanalyzer or a massspectrometer) or by different analyzers (e.g., an immunoanalyzer and amass spectrometer). The control system can control what reagent packsare used to process samples (e.g. if mass tags are desirable to use, thecontrol system could direct the sample preparation system to use a firstreagent pack with the first sample aliquot and a different, secondreagent pack containing the mass tags with the second sample aliquot).

In some embodiments of the invention, a mass analysis can be performedafter initial testing of the sample using one type of analyzer such asan immunoanalyzer. That is, the mass spectrometer can be used to performreflex testing of a sample that was previously processed by a differentanalyzer or set of analyzers including an immunoanalyzer. The systemsand methods according to embodiments of the invention also provide forthe ability to perform automated reflex testing based upon predeterminedcriteria using a control system running intelligent software. Based onwhether the results from the primary immunoassay meet certain criteria,the software can determine if the sample should be retested by the sameanalyzer (e.g., the immunoanalyzer) or reflex tested by the massspectrometer. Since the primary sample can still be “on-deck” in theimmunoanlyzer, the sample preparation for the mass spectrometricanalysis assay can be initiated if the control system determines that aretest or a reflex test is desirable or necessary. The sample processingsystem can advantageously have reagent cartridges for various thedetection processes associated with the various analyzers.

In some embodiments, two, three, or more aliquots of the primary samplecan be prepared for the different analyses performed by the differentanalyzers including the mass spectrometer. This may involve separatingthe biological sample into multiple aliquots and providing the multiplealiquots into multiple sample retention vessels, the multiple sampleretention vessels used in respective analyzers in the two or moreanalyzers. Aliquot preparation can occur in a sample staging apparatus,or it may occur within one of the analyzers.

In some embodiments, where the first analyzer used is an immunoanalyzer,after eluting an analyte originally present in the primary sample froman antibody bound to a magnetic particle, the eluant containing theanalyte can be characterized as a processed sample aliquot, since it isderived from an original sample aliquot. The processed sample aliquotcan then be analyzed by the mass spectrometer. Primary samples andprocessed sample aliquots, and any additional sample aliquots can betemporarily held in a sample storage unit (optionally, a chilled unit)while the control system determines if mass spectrometric analysis isneeded.

When the control system determines that a retest or reflex process isnecessary or desirable (due to the outcome of the analysis of aparticular condition set), and the sample needs to be processed by themass spectrometer, either a primary sample or a processed sample aliquotcan be used. A retest process may be necessary or desirable if a primaryanalysis is viewed by the control system or other entity as beinginconclusive, inadequate by itself, or incomplete. A reflex test may benecessary or desirable if the primary analysis of a first analyteindicates that further testing of one or more other analytes isdesirable.

Embodiments of the invention can provide simplified workflows fromsample preparation to a final analysis result with multiple options toimprove the sensitivity, specificity and accuracy of the sample analysisprocess. With respect to the use of a sample introduction apparatus thatis used to transfer a sample from an immunoanalyzer to a massspectrometer, embodiments of the invention can eliminate the need forutilizing centrifugation and/or HPLC (high pressure liquidchromatography) prior to any mass spectrometer analysis. In someembodiments, no centrifuge and no HPLC apparatus is present in thesample processing system.

As noted above, the sample processing system can utilize a massspectrometer to analyze a biological sample. The sample can be preparedfor a mass spectrometric analysis in any suitable manner. For example, afirst example sample preparation procedure that can be performed by thesample preparation system may include immunopurification of a targetanalyte from a primary sample using a monoclonal or polyclonal antibodyattached to a paramagnetic particle. In an immunopurification process,after the analyte is captured by the antibody, any unbound molecules arewashed away in a washing process. In a subsequent elution step, theanalyte is subsequently released from the antibody using a buffer andthe eluant. The eluant containing the “purified” target can becharacterized as a processed sample aliquot, which is then collected andanalyzed by the mass spectrometer.

The antibody that is typically used in the immunopurification processcan be replaced by alternatives, e.g. aptamers, nanoparticles, bindingproteins, etc. The immunocapture reagent can be designed to capture aspecific analyte or a specific panel of analytes, e.g., drug panel orendocrine panel, etc. In embodiments of the invention, an MRM (multiplereaction monitoring) workflow using a triple quadrupole massspectrometer, where specific parent to daughter ion transitions arepresent for each analyte, can be utilized to accurately analyze thespecific analytes in the panel. In case there are no differentiatingtransitions in tandem mass spectrometry or MS² (typically in case ofisomers or isobars), a unique transition in MS³ may be utilized todifferentiate between them.

In a second exemplary procedure performed in the sample preparationsystem, protein precipitation is used to separate proteins from smallmolecules. The proteins in a sample aliquot are precipitated using aprecipitation reagent, after which the precipitated proteins are boundto paramagnetic beads. The proteins bound to the beads can be physicallyseparated from a supernatant using a magnetic washing process. Thesupernatant liquid, which can be characterized as a processed samplealiquot, can be collected and transferred to the mass spectrometer foranalysis. Drug classes for definitive or stand-alone testing can beanalyzed using this workflow.

In some embodiments, mass spectrometric reagents such as mass tags(e.g., Amplifex™ mass tags) can be used during the sample preparationprocess to enhance signals and improve sensitivity. Mass tags aretypically designed to react specifically with functional groups commonto a specific class of analytes, e.g., keto functionality present insteroid class or diene functionality present in the Vitamin D class,etc. Mass tags can influence fragmentation of the molecule to yieldspecific fragments to provide unique transitions, which can lead to moreaccurate results. In some cases, the differential mobility of ions inthe gas phase may also be used to separate isomeric or isobariccompounds. Reagents such as this can be used with the second samplealiquot that will be processed for a mass spectrometric analysis.

Mass tags can be designed to provide accuracy in a number of ways.First, mass tags may be used to modify the differential mobility of thetagged ions (target analyte and interfering compounds) in the gas phaseand simplifying their separation based on differences in their mobilityproperties. Separating isomeric/isobaric compounds (referred to asinterfering compounds) before detection can help to improve the accuracyof any analysis results. Second, mass tags can also provide signalenhancement of the target analyte to improve sensitivity. Third, masstags can influence fragmentation of the tagged molecules to helpdifferentiate analytes and interfering compounds.

In embodiments of the invention, an internal standard of the analyte(s)can be added to the sample prior to analysis by a mass spectrometer. Theinternal standard can be an isotopic version of the analyte(s) and cancompensate for losses during the sample preparation process. The ratioof the internal standard to the analyte peak can be used forquantitation. Quantitation can be performed using an externalcalibration curve, if desired.

In addition, embodiments of the invention can use universal trap columnsand solvents, and a universal mass spectrometry source, which can makeautomation less complex. A universal trap column and source can work formost assays and will not require switching between different assays. Thesoftware in the control system can indicate when the life of theuniversal trap column is up and needs replacement. Yet other embodimentsof the invention may utilize LC (liquid chromatography) columns.

FIG. 1A shows a high level block diagram of a sample processing system100 according to an embodiment of the invention. The sample processingsystem 100 comprises a plurality of analyzers. The plurality ofanalyzers may include a first analyzer 101, a second analyzer 102, athird analyzer 107, and a mass spectrometer 106. The mass spectrometer106 is a type of analyzer. Although one mass spectrometer is shown forpurposes of illustration, it is understood that more than one massspectrometer may be present in the sample processing system 100.Further, although three analyzers 101, 102, 107 other than the massspectrometer 106 are illustrated in FIG. 1A, it is understood that therecan be fewer than three additional analyzers, or more than threeanalyzers in other embodiments of the invention.

A control system 108 may be operatively coupled to the three analyzers101, 102, 107 other than the mass spectrometer 106, as well as aninformation management apparatus 110 and a data storage component 112.Input/output interfaces may be present in each of these devices to allowfor data transmission between the illustrated devices and any externaldevices.

In this example, a sample introduction apparatus 104 may be disposedbetween the mass spectrometer 106 and the second analyzer 102. Thesample introduction apparatus 104 may be physically and/or operationallycoupled to the analyzer 102 and the mass spectrometer 106. The sampleintroduction apparatus 104 may serve to transfer processed samples orsample aliquots directly from the analyzer 102 to the mass spectrometer106. For example, the sample introduction apparatus configured totransfer a first or second processed sample aliquot from the analyzer102 to the mass spectrometer 106. Although the sample introductionapparatus 104 is shown as being present between the second analyzer 102and the mass spectrometer 106, it may alternatively or additionally beconfigured to transfer a biological sample directly between any of theanalyzers in the sample processing system 100.

In one example, the second analyzer 102 may include a number of samplealiquot processing apparatuses to form processed sample aliquots foranalysis. Such processing apparatuses may process a sample or samplealiquot in any suitable manner. Examples of sample aliquot processingapparatuses include reagent addition stations (e.g., reagent pipettingstations), sample pipetting stations, incubators, wash stations (e.g., amagnetic wash station), sample storage units, etc. The plurality ofsample aliquot processing apparatuses are capable of processing thefirst sample aliquot to form the first processed sample aliquot, andcapable of processing the second sample aliquot to form the secondprocessed sample aliquot. A “processed sample aliquot” may include asample aliquot that is processed any suitable number of times by anysuitable number of processing apparatuses.

The control system 108 can control and/or transmit messages to thefirst, second, and third analyzers 101, 102, and 107, the sampleintroduction apparatus 104, and/or the mass spectrometer 106. Thecontrol system 108 may comprise a data processor 108A, and anon-transitory computer readable medium 108B and a data storage 108Ccoupled to the data processor 108A. The non-transitory computer readablemedium 108B may comprise code, executable by the processor 108A toperform the functions described herein. Although the control system 108(as well as the information management apparatus 110) is depicted as asingle entity in FIG. 1A, it is understood that the control system maybe present in a distributed system or in a cloud-based environment.

The data processor 108A may include any suitable data computation deviceor combination of such devices. An exemplary data processor may compriseone or more microprocessors working together to accomplish a desiredfunction. The data processor 108A may include a CPU that comprises atleast one high-speed data processor adequate to execute programcomponents for executing user and/or system-generated requests. The CPUmay be a microprocessor such as AMD's Athlon, Duron and/or Opteron, IBMand/or Motorola's PowerPC; IBM's and Sony's Cell processor, Intel'sCeleron, Itanium, Pentium, Xeon, and/or XScale; and/or the likeprocessor(s).

The computer readable medium 108B and the data storage 108C may be anysuitable device or devices that can store electronic data. Examples ofmemories may comprise one or more memory chips, disk drives, etc. Suchmemories may operate using any suitable electrical, optical, and/ormagnetic mode of operation.

The computer readable medium 108B may comprise code, executable by thedata processor 108A to perform any suitable method. For example, thecomputer readable medium 108B may comprise code, executable by theprocessor 108A, to cause the sample processing system 100 perform amethod including determining, in response to receipt of a test order totest a biological sample, one or more condition sets of the plurality ofcondition sets in the data storage component to use to complete the testorder; determining an analyzer or analyzers from the plurality ofanalyzers to use to process the biological sample based on the one ormore condition sets, and one or more parameters in the plurality ofparameter lists, the determined analyzer or analyzers including the atleast one mass spectrometer; and causing the determined analyzer oranalyzers of the plurality of analyzers to process the biological sampleto determine one or more measurement values for the biological sample.

The system 100 may also comprise a data storage component 112. The datastorage component 112 may store parameters 112A and condition sets 112B.The data storage component 112 may be internal or external to thecontrol system 108 or the information management apparatus 110. The datastorage component 112 may include one or more memories including one ormore memory chips, disk drives, etc. The data storage component 112 mayalso include a conventional, fault tolerant, relational, scalable,secure database such as those commercially available from Oracle™ orSybase™.

The parameters 112A in the data storage component 112 may include anyfactor that relates to a condition of operation of an instrument such asan analyzer. Parameters may relate to detection ranges for differentanalyzers, types of measurement values obtainable by the analyzers, theavailability of the analyzers, the cost of performing an operation on ananalyzer, etc. The parameters 112A may include static (e.g., detectioncapabilities of analyzers) and/or dynamic information (e.g., the currentavailability of an analyzer or when it will be available). With respectto dynamic information, the control system 108 may receive data fromeach of the analyzers 101, 102, 107, and the mass spectrometer 106 on aregular basis to provide updated parameters 112A. For example, signalsmay be provided to the various analyzers 101, 102, 107 or the massspectrometer 106 indicating that they are idle or busy and thisinformation may be provided by the control system 108 to the datastorage component 112.

The condition sets 112B may include a set of rules for handling specifictypes of biological samples. Each condition set may include a pluralityof variables. Laboratory rules may include those for handling samples,detection ranges needed to meet order, etc. As noted above, conditionsets may include one or more rules that can be used to determine whichanalyzer or combination of analyzers to select to process a biologicalsample. The rules may be associated with the biological sample and/ormay incorporate data unrelated to the specific biological sample.

In some embodiments, condition sets 112 may include one or more rulesthat will cause the control system 108 to select the mass spectrometer106 to analyze the biological sample. For example, a test order to testfor a presence of at least one drug or metabolite thereof or both in abiological sample may be received by the sample processing system 100.At least one condition set of the at least two condition sets maycomprise a rule that causes the control system to select the massspectrometer from the plurality of analyzers in the system to analyzethe biological sample for the drug or the metabolite. The at least onedrug may include a therapeutic drug, a drug of abuse, and/or animmunosuppressant drug.

The sample processing system 100 may also comprise an informationmanagement apparatus 110. The information management apparatus 110 maybe coupled to the control system 108, and may be configured to (i) storepatient information, (ii) receive one or more test orders for thebiological sample, and (iii) receive the one or more measurement valuesof the biological sample from the plurality of analyzers 101, 102, 107,including the mass spectrometer 106.

The information management apparatus 110 may comprise a data processor110A and a non-transitory computer readable medium 110B. The computerreadable medium 110B may comprise code for causing the data processor110A to receive from the analyzer or analyzers 101, 102, 106, 107, theone or more measurement values for the biological sample, compare theone or more measurement values to patient information 110C-1 stored in adata store in a data storage 110C, and provide an output aftercomparing. The patient information 110C-1 in the information managementapparatus 110 may be a patient information repository. The dataprocessor 110A and the non-transitory computer readable medium 110B maybe of the same or different type than the data processor 108A and thecomputer readable medium 108B in the control system 108.

The information management apparatus 110 may also comprise a datastorage 110C, which may store patient information 110C-1, test orders110C-2, and measurement values 110C-3. The information managementapparatus 110 may also include one or more input devices 110D and outputdevices 110E. Input devices may include touchscreens, keyboards,pointers, microphones, etc. Output devices 110E may include speakers,displays, and tactile devices.

In some embodiments, the information management apparatus 110 may beconfigured to compare the presence or absence of a drug or metabolite ina biological sample, as determined by the mass spectrometer 106 or anyof the other analyzers 101, 102, 107 to patient information 110C-1 inthe data storage 110C. As a result of this comparison, an output may beprovided by the information management apparatus 110 via an outputdevice such as a display coupled to the data processor 110A.

The output may be of any suitable type. For example, the output mayrelate to a report that combines the measurement values from theanalyzers 101, 102, 107, and/or the mass spectrometer 106 with patientinformation 110C-1 such as the name of the patient or medical recordnumber of the patient. In other embodiments, the output may include theresult of a comparison of any or proposed medications of the patent toany measurement values to the measurement values. In yet otherembodiments, the output might be a diagnosis or recommendation basedupon the measurement values obtained from the analyzers and the patientinformation 110C-1. In other embodiments, an output from the analyzers101, 102, 107 or the information management apparatus 110 may be in formof images (e.g., a hematology analyzer could output an image of a cell).

In some embodiments, the information management apparatus 110 mayinclude a laboratory information system (LIS), a hospital informationsystem (HIS), and middleware. The analyzers 101, 102, 107, and the massspectrometer 106 may be connected directly to the LIS over a network.Data (e.g., measurement values) generated by analyzers 101, 102, 107,and the mass spectrometer 106 can be transmitted to the LIS or HIS. Amiddleware hub may be inserted into this data flow on the communicationpath between the analyzers 101, 102, 107, and the mass spectrometer 106.The LIS, with an information system interface, allows for communicationsbetween the LIS and the middleware hub. In some implementations, themiddleware hub may provide additional instructions to the analyzers 101,102, 107, and the mass spectrometer 106 in order to create, cancel, ormodify test orders for the analyzers 101, 102, 107, and the massspectrometer 106 to execute. In some embodiments, the middleware hub mayinclude the control system 108 or may include software running on thecontrol system 108.

The sample processing system 100 may also include an optional samplestaging apparatus 140 that may be operatively coupled to the controlsystem 108, as well as the first analyzer 101, the second analyzer 102,the sample introduction apparatus 104, the mass spectrometer 106, andthe third analyzer 107. The sample staging apparatus 140 may include anynumber or type of device that is needed to prepare or transportbiological samples to the the first analyzer 101, the second analyzer102, the sample introduction apparatus 104, the mass spectrometer 106,and/or the third analyzer 107.

FIG. 1B shows a block diagram of some components that may be in anexemplary sample staging apparatus 140. The sample staging apparatus 140may include a sample presentment unit 140A for receiving sample tubeswith biological samples, a sample storage unit 140B for temporarilystoring sample tubes or sample retention vessels, and various transportdevices 140C. The transport devices 140C may be for transporting sampletubes or sample retention vessels to and from the first analyzer 101,the second analyzer 102, the sample introduction apparatus 104, the massspectrometer 106, and/or the third analyzer 107. Examples of transportdevices may include conveyors, sample tracks, pick and place grippers,laboratory transport elements that can move independently (e.g., pucks),and other tube conveying mechanisms. The sample staging apparatus 140may also include one or more aliquotters 140D for aliquotting biologicalsample from a sample tube to a sample retention vessel, and a samplevessel module 140E for holding empty retention vessels. The samplestating apparatus 140 may also include a waste module 140F forcollecting waste or spent sample retention vessels or sample tubes.

FIG. 1C shows a flowchart illustrating a method according to anembodiment of the invention. In one embodiment of the invention, themethod is performed by a sample processing system. The sample processingsystem includes a plurality of analyzers comprising at least one massspectrometer, at least one data storage component storing a plurality ofcondition sets, the condition sets in the plurality of condition setsdiffering by at least one variable, and a plurality of parameter listsfor the plurality of analyzers. The sample processing system alsoincludes a control system coupled to the plurality of analyzers, and theat least one data storage component.

In step 160, a test order is received at the information managementapparatus 110 of the sample processing system 100. The test order may bestored with other test orders 110C-2 in the data storage 110C in theinformation management system 110. The test order may be received by theinformation management apparatus 110 via an input device 110D in theinformation management apparatus 110.

In step 162, before or after step 160, a biological sample is receivedby the sample processing system 100. In some embodiments, the biologicalsample is received at the sample staging apparatus 140. The biologicalsample may be present in a sample tube and placed in the samplepresentment unit 140A of the sample staging apparatus 140.

In step 164, the control system 108 determines, in response to receiptof the biological sample and the test order, one or more condition setsfrom a plurality of condition sets stored in the data storage component112 to use to process the biological sample. As an illustration, thetest order may request that a biological sample of blood be tested forthe presence or amount of a particular drug of abuse. The test order mayfurther request that the test be performed within a particular period oftime, and that the test result have a predetermined degree ofconfidence. An exemplary condition set may be selected, based upon theinformation in the test order and information relating to the biologicalsample. For example, the control system 108 may determine that if thebiological sample is blood, and if the predetermined confidence level isto be achieved, then the second analyzer 102 which may be animmunoanalyzer, and the mass spectrometer 106 are selected to analyzethe biological sample. Any other analyzers that may be suitable toachieve the end result may also be included in the list of candidateanalyzers.

In step 166, before or after step 164, the control system 108 analyzesthe parameter lists relative to the information in the test order todetermine the appropriate analyzer or combination of analyzers thatwould be suitable to process the biological sample according to the testorder. The control system 108 may evaluate whether the requested test tobe performed can be performed by the analyzers in the sample processingsystem 100. For example, continuing with the above example, the testorder may request a determination as to the presence or amount of aparticular drug of abuse in a biological sample. Given this information,the control system 108 may determine that only the second analyzer 102and the mass spectrometer 106 would have the requisite sensitivity totest for that particular drug of abuse. Thus, the desired sensitivityfor the test to be performed can be compared the sensitivities of theanalyzers in the parameters 112A.

In step 168, one or more analyzers are determined. The determined one ormore analyzers are then used to process and analyze the biologicalsample. In some embodiments of the invention, the control system 108 maydetermine that two or more of analyzers will be used to process thebiological sample. At least one of the analyzers is a mass spectrometer.The determination of which analyzers can be used to process thebiological sample can depend upon a number of factors and can be basedon the previously described parameters 112A and condition sets 112B. Insome embodiments, the selection may specifically depend upon theaccuracy of the results provided by the various analyzer types in thesystem, the availability of the analyzers systems, and any specificrequirements of the test order for the biological sample.

In step 170, the biological sample is then processed and analyzed by oneor more analyzers that were determined in step 168. Depending upon whichanalyzer or combination of analyzers was selected by the control system108, any necessary sample preparation for the analyzers may take placewithin the sample staging apparatus 140, or it can be performed withinthe analyzers 101, 102, 107, or the mass spectrometer 106. The controlsystem 108 may provide instructions to any of the determined analyzers101, 102, 107 and/or mass spectrometer 106. In some embodiments, thecontrol system 108 may maintain communication with the determinedanalyzers 101, 102, 107 and/or mass spectrometer 106 to control themduring processing and analyzing the biological sample. In otherembodiments, the control system 108 may provide an initiationinstruction, and the analyzers 101, 102, 107 and/or mass spectrometer106 may thereafter operate independently of the control system 108 untilmeasurement values are produced by them.

In step 172, one or more measurement values are determined for thebiological sample by the one or more analyzers. Each analyzer 101, 102,107, or the mass spectrometer 106 may produce one or more measurementvalues.

In step 174, the one or more measurement values are provided from theanalyzers to the information management apparatus 110, and may be storedin the data storage 110C along with other measurement values 110C-3. Themeasurement values may be transmitted from the analyzers to theinformation management apparatus 110 via the control system 108, ordirectly.

In step 176, after the measurement values are received by theinformation management apparatus 110, an output is provided from theinformation management apparatus 110. For example, the measurementvalues obtained from the biological sample may be compared to patientinformation 110C-1. For example, the output may relate to a report thatcombines the measurement values from the analyzers 101, 102, 107, and/orthe mass spectrometer 106 with patient information 110C-1 such as thename of the patient or medical record number of the patient. In otherembodiments, the output may be the result of a comparison of any orproposed medications of the patent to any measurement values to themeasurement values. In yet other embodiments, the output might be adiagnosis or recommendation based upon the measurement values and thepatient information 110C-1

In step 178, the control system 108 determines if another biologicalsample is to be processed. If there is, then the process continues backto step 160. If not, then the process can end.

FIG. 2 shows a diagram illustrating different processing paths that canbe taken between an analyzer such as an immunoanalyzer, and a massspectrometer, in a sample processing system according to embodiments ofthe invention. A high level process flow may include a samplepreparation processing module 210, a sample introduction processingmodule 230, and a sample detection processing module 240.

The sample preparation processing module 210 may include process stepsthat process a sample containing an analyte such that it may be detectedduring the sample detection processing module 240. In embodiments of theinvention, the sample preparation processing module 210 may include animmunoprecipitation or immunopurification process. For purposes ofillustration, steps in the sample preparation processing module 210 maybe carried out in the second analyzer 102. Steps in the sampleintroduction process module may be carried out in the second analyzer102, the mass spectrometer 106, or it may be a separate, stand-aloneapparatus separate and apart from the analyzer 102 and the massspectrometer 106. The sample detection process module 240 can beperformed in the mass spectrometer 106 and/or an immunoanalyzer.

The sample introduction process module 230 includes process steps thatcan transfer a sample containing an analyte from the second analyzer 102to the mass spectrometer 106. Also, the sample introduction processmodule 230 may include the transfer of a sample without additionalseparation 232 and with additional separation 234. Specific sampleintroduction processes that do not include additional separation 232 mayinclude flow injection 232A or SPME (solid phase micro extraction)/OPP(open port probe) 232B. Sample introduction processes that can includeadditional separation can include a trap and elute process module 234A.An optional DMS (differential mobility spectrometry) process module 238may be carried out downstream of the sample introduction process module230 after the sample has been ionized but prior to the sample being massanlazyed.

The direct flow injection process module 232A may utilize an apparatusthat can include a direct injection apparatus that can directly inject aprocessed sample from an analyzer into a mass spectrometer. Theapparatus may include a carrier solution source, which may be used tocarry the processed sample to the mass spectrometer. A pump such as aperistaltic pump may be included in the direct flow injection apparatus.

The SPME/OPP process module 232B can utilize an SPME device and an OPPapparatus, which may include an open port sampling interface. SPME canintegrate sampling, sample preparation, and extraction into a singlesolvent-free step. Generally, an SPME device utilizes a fiber or othersurface (e.g., blades, micro-tips, pins, or mesh) coated with anextracting phase to which analytes within the sample can bepreferentially adsorbed when the device is inserted into a samplealiquot or processed sample aliquot. An SPME device can be proximate toan OPP, which can be a vertically aligned, co-axial tube arrangementenabling solvent delivery to a sampling end (open-port) through thetubing annulus and aspiration down the center tube into an ion sourcedriven by a nebulizer gas.

The trap and elute process module 234A may utilize a trap and eluteapparatus. The trap and elute process module 234A can involve injectinga sample into a small-volume column where analytes of interest areconcentrated before elution into the mass spectrometer. The trappingprocess optimizes sensitivity and selectivity, and improves robustness.Schematic diagrams of exemplary trap and elute apparatuses are shown inFIGS. 7A and 7B, which are described in further detail below.

In other embodiments, instead of a trap and elute process module, ahydrocarbon (e.g., C18) coated tip can be used. Such tips arecommercially available.

The sample introduction process module 230 could also include mechanicalreaction vessel transport devices. Such transport devices may includepick and place apparatuses such as pick and place transfer gantrys,transfer shuttles such as extended linear reaction shuttles, orcombinations of the pick and place transfer gantrys and extended linearreaction shuttles.

The sample detection process module 240 may include steps that are usedto detect the presence, absence, and/or quantity of a particular analytein a sample. The sample detection process module 240 may include the useof a mass spectrometric process module 240A and/or an optical detectionprocess module 240B. The optical detection process module 240B may use achemiluminescence or fluorescence based detection process. Other detailsregarding the mass spectrometric process module 240A and the opticaldetection process module 240B are provided below.

FIG. 3 shows a high level flowchart 300 illustrating the different typesof detection processes that can be performed using the sample processingsystem according to embodiments of the invention. In the flowchart 300,the ability to detect the presence, absence, and/or concentration of aparticular analyte using an optical detection process and a massspectrometric process is shown. It is apparent that embodiments of theinvention have a great deal of flexibility in determining if an analyteis or is not present in a particular sample.

In step 302, an analyzer can obtain two or more or more sample aliquotsof a sample and can dispense them into two or more reaction vessels. Ifthe analyzer is an immunoanalyzer, one of the sample aliquots may besubjected to an immunoassay test in the immunoanalyzer at step 304. Afirst reaction vessel including a first sample aliquot may be processedby the immunoanalyzer to form a first processed sample aliquot. Then,the immunoanalyzer may be used to detect if a particular analyte ispresent or absent in the first processed sample aliquot in the reactionvessel.

After the immunoassay test is performed on the first processed samplealiquot, the control system in the sample processing system can make adecision as to whether a confirmatory test is desired in step 306. If aconfirmatory test is desired, the second sample aliquote in the thesecond reaction vessel can be processed by the analyzer to form a secondprocessed sample aliquot. The second processed sample aliquot may betransferred from the analyzer to a mass spectrometer in step 314. Oncethe processed second aliquot is in the mass spectrometer, the massspectrometer may perform a mass analysis on the processed second aliquotin step 310. After the mass analysis is performed on the processedsecond aliquot, a report may be generated in step 312. If a confirmatorytest is not desired, then a report may be generated in step 308 withoutperforming a mass spectrometric analysis in step 310.

In some embodiments, data from the immunoanalyzer may indicate that theconcentration of the analyte in the first processed sample aliquot isbelow, above or equal to a predetermined threshold in a primaryanalysis. The control system may then have determined that a reflexprocess on the sample may be desirable or necessary. The method may thenfurther include causing the analyzer to process a second aliquot of thesample to form the second processed sample aliquot. The sampleintroduction apparatus may transfer the second processed sample aliquotfrom the analyzer to the mass spectrometer. The control system may thencause the mass spectrometer to detect the presence of one or more otheranalytes in the second processed sample aliquot in a secondary analysis.

In some cases, the detection of the analyte in the primary analysis mayindicate that a particular condition (e.g., a medical condition) may bepresent. However, to confirm that the particular condition is present,the secondary analysis may analyze for a second analyte using massspectrometry. Together, the presence or absence of the first and secondanalytes may indicate that the presence of the particular condition ispresent.

The above described threshold may be any suitable value. For example,the threshold may be that a predetermined quantity (e.g., amount) orconcentration of a particular analyte(s) needs to be present in aprocessed sample aliquot before it can be concluded with a degree ofconfidence that the analyte is or is not present in the processed samplealiquot.

The use of the mass spectrometric analysis in a reflex process isdesirable. In some instances, when a sample is tested for an analyte ina traditional immunoanalyzer, non-specific binding can occur on theantibodies and/or the magnetic beads to which they are attached. Thismay affect the accuracy of the analysis being conducted. Massspectrometric analyses are not subject to the problems associated withnon-specific binding, and can thus serve as an effective mechanism forreflex testing, or testing in general.

FIG. 4A shows a block diagram of an automated immunochemistry analyzer400 that can be used in an automated sample processing system accordingto an embodiment of the invention. The basic structural and functionalmodules of the automated immunochemistry analyzer 400 can include asample presentation unit 401, a main sample pipetting station 402, abulk vessel feeder 403, first dual reagent pipetting stations 404 and405, second dual reagent pipetting stations 406 and 407, a firstpick-and-place gripper 408, a second pick-and-place gripper 409, a thirdpick-and-place gripper 410, an incubator/wash/read station 412, a samplestorage 411, and a reagent storage 413. Optionally, the sample and/orreagent storage can be chilled.

The sample presentation unit 401 can used to transport an entirerequired test sample to and from the main sample pipetting station 402.A detailed description of the configurations and functions of the samplepresentation unit 401 is provided in U.S. Pat. No. 6,790,413, filed onMay 3, 2001, which is incorporated herein by reference in its entirety.

The main sample pipetting station 402 can be used to aspirate samplesout of the sample tubes and dispense them into reaction vessels suppliedby the bulk vessel feeder 403. A detailed description of theconfigurations and functions of the bulk vessel feeder 403 is providedin U.S. Pat. No. 6,790,412, filed on Feb. 6, 2001, which is incorporatedherein by reference in its entirety.

The four reagent pipetting stations 404, 405, 406, and 407 can be usedto mix a sample with reagents for subsequent assays. The four reagentpipetting stations 404, 405, 406, and 407 can be arranged as two dualpipetting stations and can be independent to each other. Each of thefour reagent pipetting stations 404, 405, 406, and 407 can have its ownfluid pumps and valves, wash towers, reaction vessel carriages, andpipettor(s). Although four pipetting stations 404, 406, 406, 407 areillustrated, it is understood that embodiments of the invention caninclude more or less of the pipetting stations.

The three vessel pick-and-place grippers 408, 409, 410 can be used totransport sample and reaction vessels among the various modules of theanalyzer. The first pick-and-place gripper 408 can be used to transportreaction vessels between the bulk vessel feeder 403 or the samplestorage 411 and the reagent pipetting stations 404, 405, 406, 407. Thesecond pick-and-place gripper 409 can be used to transport reactionvessels between the reagent pipetting stations 404, 405, 406, 407 andthe incubator of the incubator/wash/read station 412. The thirdpick-and-place gripper 410 is used to transport reaction vessels betweenthe incubator and the wash wheel (an example of a wash station) of theincubator/wash/read station 412. A detailed description of theconfigurations and functions of the vessel pick-and-place grippers 408,409, and 410 is provided in U.S. Pat. No. 7,128,874, which is hereinincorporated by reference in its entirety. It is understood thatembodiments of the invention can have more or less pick-and-placegrippers.

The sample storage 411 can be used for storing the samples contained inthe reaction vessels at a low temperature for a certain period of time,e.g., up to three (3) hours, so that the samples may be used forretesting or reflex testing. When a test is requested on a patientsample, the test outcome may drive a request for additional testing. Asnoted above, this automatic request for additional tests is reflextesting. The time delay from the first aspiration to knowing if anothertest will be started can range to as long as 45 minutes or more. To holda sample tube for such a period of time prevents the sample from beingused in other places. If the tube is passed to other instruments, it maybe difficult for a laboratory technician to find the tube and reload iton the instrument requesting the reflex test. To allow a single quicksample draw on sample tubes that might require reflex testing, a singleaspiration (aliquot) can be taken with sufficient test material for thepossible reflex test(s). However, to insure that the test materials donot evaporate or deteriorate, the aliquot may need to be refrigerated onboard the analyzer.

The sample storage 411 can one or more reaction vessels containingsample aliquots for samples that are being processed in primaryanalyses. The sample aliquots stored in the sample storage 411 can beused to perform secondary analyses (e.g., reflex tests) on either theanalyzer or the mass spectrometer.

Referring to FIG. 4C, there is shown the arrangement of the main samplepipetting station 402 and the sample storage 411 of the automatedimmunochemistry analyzer. The pipettor of the main sample pipettingstation 402 first aspirates samples from sample tubes, and then movesinto a position above the sample storage 411. Meanwhile, the samplestorage 411 first receives an empty reaction vessel from the bulk vesselfeeder 403 by the pick and place gripper 417, and then moves the emptyreaction vessel under the pipettor of the main sample pipetting station402. The aspirated sample is then dispensed into the chilled reactionvessel. Insulation and doors 418 are provided to control the environmentin the sample storage 411. The sample storage 411 can be a precisioncontrolled refrigerator with multiple storage locations 419 capable ofreceiving and transferring reaction vessels for or filled with samplematerial. Sample aliquots can be present in reaction vessels that arestored in the sample storage 411. These samples can be used forretesting or reflex testing in the immunoanalyzer or in the massspectrometer.

The incubator/wash/read station 412 can be used for the incubating,washing, and reading steps of the assays. In some embodiments, theincubator/wash/read station 412 may be generically characterized as aseparation station. It may include one or more incubators, one or moreassay wash stations, and one or more readers, such as a photomultipliertube (PMT) detector, or other optical detection systems. A detaileddescription of the configurations and functions of theincubator/wash/read station is provided in U.S. Pat. No. 7,217,391,filed on Mar. 16, 2001, which is herein incorporated by reference in itsentirety.

As a way of minimizing background signals from excess or unboundmaterials, immunoassays generally use one or more separation phases becarried out in the reaction vessel. To facilitate the separation orwashing process, a variety of techniques can be used, including, but notlimited to, well coating techniques, bead coating techniques, or the useof paramagnetic particles. Each of these separation media are coatedwith a capture reagent (e.g., antibody) that will bind analyte moleculesof interest in a sample. When paramagnetic particles are used as theseparation media, the paramagnetic particles are pulled to the wall ofthe reaction vessel by magnets during the washing process and thesupernatant is aspirated. Luminescent labels are then bound to theseanalyte molecules. When a luminescing reagent or substrate is added tothe reaction vessel, it reacts with the luminescent label to producelight that is detectable by the analyzer's optical detection station.

The reagent storage 413 can be used for storing reagents used for theimmunoassays as well as the mass spectrometric process. The reagentpacks may include reagents that are in liquid or solid form. The reagentstorage 413 can store reagent packs in a refrigerated environment untilrequested for use, transfer a pack to an appropriate reagent pipettingstation when requested for use, and return the pack to storage whenpipetting is complete. It can also return a full or partially used packto the operator when requested and automatically dispose of empty packs.The temperature in the reagent storage 413 can be controlled by Peltierdevices and monitored with a thermistor.

For immunoassays, some types of reagents can include paramagneticparticles with or without coating of antibodies or antigens, blockingagents, antibodies, assay buffers, antibodies conjugated to enzymes (forchemiluminescence), sample pre-treatment reagents such as acids, bases,or releasing agents.

For mass spectrometry, mass spectrometric reagents such as mass tags(e.g., Amplifex™ mass tags) can be used during the sample preparationprocess to enhance signals and improve sensitivity. As noted above,reagents such as this can be used with the second sample aliquot thatwill be processed for a mass spectrometric analysis.

The reagent packs can be loaded into the reagent storage 413 as follows:(a) an input tray cover is opened by the operator and the input tray ispositioned, if necessary, to allow the operator to place reagent packsinto the tray; (b) the input tray cover is closed and the input traycloses, bringing the reagent packs into the reagent storage 413; (c) asthe input tray closes, each reagent pack position passes a bar codereader (BCR), where each of the four pack positions is read andidentified, (d) a reagent pack gripper of a reagent pack transportingand sorting mechanism moves to get a pack from the input tray that wasidentified by the bar code reader; (e) the reagent pack gripper of thereagent pack transporting-and-sorting mechanism moves the reagent packto either a storage location or a pipetting location (if needed), anddrops the reagent pack off, and (f) the above steps (d) through (e) canbe repeated, until all reagent packs are removed from the input tray.

The reagent storage 413 includes a mechanism for transporting andsorting multiple reagent packs. A detailed description of theconfiguration and functions of such a mechanism for transporting andsorting multiple reagent packs is provided in U.S. Pat. No. 6,746,648,filed on Jun. 15, 2000. Other structures and functions of the reagentstorage 413 conform to existing arrangements known to those of ordinaryskill in the art, and therefore will not be described in detail here.

FIG. 4B shows an illustrative flow chart diagram showing the basicoperating procedures of the method of automated immunochemistryanalysis.

The basic operating procedures of the automated immunochemistry analysiscan be carried out in three main sections of the automatedimmunochemistry analyzer: a sample aliquoting section 414, where thesample is aspirated out of a sample tube and dispensed into a reactionvessel, a reagent pipetting section 415, where the sample is mixed withreagents, and an incubate/wash/read section 416, where the mixed sampleis incubated, washed, and separated from particulates and read by thephoto-multiplier tube (PMT) detector or other optical detection station.

The sample aliquoting section 414 and the incubate/wash/read section 416each has one set of units, and works on a cycle (in one embodiment, anine (9)-second cycle). The reagent pipetting section 415 can have four(4) independently working reagent pipetting stations, where each reagentpipetting station works on second cycle (in one embodiment, a thirty-six(36) second cycle).

However, the scheduling of the four reagent pipetting stations can bestaggered (in one example, nine (9) seconds apart). For example, theanalyzer can accept one (1) test sample in every nine (9) seconds, i.e.,the analyzer has an effective cycle of nine (9) seconds. Accordingly,the analyzer can have a fast throughput (e.g. four hundred (400) testsper hour). Embodiments of the invention are not limited to these timingsor values.

Referring to FIGS. 4A and 4B, the basic operating procedures of thesample aliquoting section 414, the reagent pipetting section 415, andthe incubate/wash/read section 416 and are described below:

-   -   A. The Operating Cycle of the Sample Aliquoting Section 414    -   1. The user loads a sample rack containing up to four (4) sample        tubes on the sample presentation unit 401.    -   2. The rack is advanced into the main sample pipetting station        402 where the sample may be identified by a bar code reader        (BCR) and presented to the main sample pipetting station 402.    -   3. At the same time, the bulk vessel feeder 403 presents the        reaction vessel necessary for the tests to a sample reaction        vessel carriage, from where the first pick-and-place gripper 408        picks the reaction vessel up and stores it in the sample storage        411 and/or in the reaction vessel carriage of any one of the        available reagent pipetting stations 404, 405, 406, 407.    -   4. The main sample pipetting station 402 aspirates the amount of        sample required and aliquots it into the reaction vessel in the        sample storage 411, and afterwards, the probe is washed in its        dedicated wash station. The sample probe can be washed to reduce        sample carry-over to a level that will not adversely affect        other samples.    -   B. The Operating Cycle of the Reagent Pipetting Section 415    -   1. The first pick-and-place gripper 408 picks up the reaction        vessel containing the aliquoted sample and moves it over to an        available reagent pipetting station.

The following describes this process: (a) a requested reaction vessel inthe sample storage 411 is positioned under an operating position of thefirst pick-and-place gripper 408; (b) a reaction vessel carriage of anavailable reagent pipetting station is positioned under anotheroperating position of the first pick-and-place gripper 408; and (c) thefirst pick-and-place gripper 408 transfers the requested reaction vesselfrom the sample storage 411 to the reaction vessel carriage of theavailable reagent pipetting station.

-   -   2. At the same time, the reagent storage 413 brings a required        reagent pack to the same reagent pipetting station.    -   3. With the reagent pack and reaction vessel in position, the        reagent pipettor of that reagent pipetting station aspirates a        required amount of sample from the sample reaction vessel and        dispenses it into an assay reaction vessel and also retrieves a        required amount of reagent from the reagent pack and dispenses        it into the assay reaction vessel, and afterwards, the probe is        washed in its dedicated wash station.

The following describes the process of sample aspiration. (a) thereagent pipettor of the reagent pipetting station is positioned over thereaction vessel; (b) an ultrasonic level sense circuit is used to detectthe surface of the sample, and lowering of the pipettor is halted oncethe surface is found and the pipettor is just deep enough to draw theneeded sample volume (therefore reducing carry-over); and (c) the sampleis drawn up using the precision pump and valve, where an in-linepressure profile is collected by using a pressure sensor during thesample aspiration, which profile can be used to verify proper samplepickup. A detailed description of the configurations and functions of aprecision pump and valve that are used herein are provided in U.S. Pat.Nos. 6,520,755 and 6,843,481, which are herein incorporated by referencein their entirety.

The following describes the process of reagent aspiration: (a) thereagent pipettor of the reagent pipetting station moves to theappropriate reagent well location of the reagent pack; (b) the reagentpipettor is lowered into the reagent pack well, and if this is aparticle well, then an ultrasonic mix circuit is enabled (and the locksignal is checked to ensure proper operation) to mix the particles priorto aspiration; and (c) the reagent is drawn up using the precision pumpand valve, where an in-line pressure profile is collected by using apressure sensor during the reagent aspiration, which profile is used toverify proper reagent pickup.

The following describes the process of a sample or reagent delivery. (a)the reagent pipettor of the reagent pipetting station moves to the assayreaction vessel location in the reaction vessel carriage of thepipetting station; (b) the reagent pipettor is lowered into the assayreaction vessel, where the exact dispense height is calculated to havethe sample or reagent just touch the probe after it has been dispensed(to ensure that there is no sample or reagent drop left on the tip ofthe probe); and (c) the sample or reagent is dispensed using theprecision piston pump and valve, where an in-line pressure profile iscollected by using a pressure sensor during the sample delivery, whichprofile is used to verify proper sample or reagent delivery.

The following describes the process of sample dilution: (a) theappropriate sample reaction vessel is retrieved for pipetting; (b) thedilution location in a reagent vessel carriage of an available reagentpipetting station is positioned under the operating position of thefirst pick-and-place gripper 408; (c) the bulk vessel feeder suppliestwo empty vessels (the reaction vessel and the dilution vessel); (d) thefirst pick-and-place gripper 408 transfers both vessels simultaneouslyto the reagent vessel carriage of the available reagent pipettingstation; (e) the sample is aspirated and delivered to the dilutionvessel along with an additional volume of buffer using the precisionpiston pump and valve, where the exact dispense height is calculated tohave the diluted sample just touch the probe after it has been dispensed(to ensure that there is no sample drop left on the tip of the probe) orto go slightly deeper if mixing is requested (in such case, theultrasonic mix circuit is enabled and the lock signal is checked toensure proper operation); (f) a specific volume of this diluted sampleis aspirated using the precision pump and valve, where an in-linepressure profile is collected by using a pressure sensor during theaspiration, which profile is used to verify proper diluted samplepickup; (g) the original reaction vessel is returned to the samplestorage 411 if there is sample left or is disposed of if it is empty;and (h) the vessel containing the diluted sample now becomes thereaction vessel for the subsequent assay being processed.

The following describes the process of sample and reagent addition: (a)the requested sample is retrieved from the sample storage 411; (b) thebulk vessel feeder supplies an empty reaction vessel to the vesselsupply carriage, (c) the vessel supply carriage is positioned under theoperating position of the first pick-and-place gripper 408; (d) thereagent vessel carriage of an available reagent pipetting station ispositioned under the other operating position of the firstpick-and-place gripper 408; (e) the first pick-and-place gripper 408transfers the empty reaction vessel to the reagent vessel carriage ofthe available reagent pipetting station; (f) the reagent vessel carriageis positioned for pipetting; (g) the requested reagent pack is alsopositioned for pipetting; (h) the reagent pipettor of the reagentpipetting station moves to a reagent wash tower, then down into thereagent wash tower, for washing the probe; (i) the sample is aspiratedand delivered to the reaction vessel; (j) the reagent pipettor moves tothe reagent wash tower, then down into the reagent wash tower, forwashing the probe; (k) the reagent pipettor aspirates the appropriateamount of reagent and delivers it to the reaction vessel; (l) the abovesteps (j) and (k) are repeated until all of the reagents have beendelivered to the reaction vessel; (m) if reaction vessel mixing isdesired, the probe moves down slightly and the ultrasonic mix circuit isenabled and the lock signal is checked to ensure the proper operation,(n) the reagent vessel carriage is positioned under an operatingposition of the second pick-and-place gripper 409; (o) an empty positionon a reaction vessel incubator wheel is positioned under anotheroperating position of the second pick-and-place gripper 409; (p) thesecond pick-and-place gripper 409 transfers the reaction vessel into theincubator of the incubating/wash/read station 412; (q) in the case oftwo or three step assays, the second pick-and-place gripper 409 willbring the reaction vessel back to a pipetting location and additionalreagents will be added, and then the vessel is transferred back to theincubator of the incubating/wash/read station 412 by the secondpick-and-place gripper 409 for the second or third incubation.

The reagent probe can be washed to reduce sample and reagent carry-overto a level that will not adversely affect other samples or reagent. Thefollowing describes this process: (a) the ultrasonic circuit is enabledto wash the reagent probe; (b) a vacuum pump evacuates the tower, whilethe tower's evacuation line pressure is monitored to ensure that thetower is draining properly; (c) the probe is flushed internally withbuffer using the precision pump and precision valve and showeredexternally using the peristaltic pump; and (d) the buffer flow isstopped while the vacuum pump and ultrasonic circuit run slightly longerto ensure that the probe is dried

-   -   4. The second pick-and-place gripper 409 picks up the assay        reaction vessel containing the mixture of sample and reagent and        moves it over to an incubator wheel of the incubator/wash/read        station 412.    -   5. The first pick-and-place gripper 408 picks up the sample        reaction vessel containing the remaining aliquoted sample and        returns it to the sample storage 411 if reflex testing is        required or else ejects it to a waste container.

The following describes this process: (a) a sample storage location inthe sample storage 411 is positioned under the operating position of thefirst pick-and-place gripper 408; (b) the reaction vessel carriage ofthe reagent pipetting station is positioned under the other operatingposition of the first pick-and-place gripper 408; and (c) the firstpick-and-place gripper 408 transfers the sample reaction vessel from thereaction vessel carriage of the available reagent pipetting station tothe sample storage 411.

-   -   C. The Operating Cycle of the Incubate/Wash/Read Section 416    -   1 The assay vessel remains in the incubator wheel for a        programmed time at a controlled temperature with heater elements        and is monitored with a thermistor, and then picked up by the        third pick-and-place gripper 410 for washing.    -   2. The wash/read ring has multiple aspirate stations and        multiple dispense stations and the assay reaction vessel goes        through several operations, including particle washing,        substrate addition and incubation, etc., under a controlled        temperature with heater elements and monitored with a        thermistor.    -   3 The assay reaction vessel is read by the reader/detector, and        thereafter is put back to the incubator by the third        pick-and-place gripper 410, and thereafter picked up and        disposed in the waste container by the second pick-and-place        gripper 409.

The operations of the analyzer are supported by fluid systems,electronic control hardware; and software, including various sensors andmicro-controller(s), electrical power supply units, motors, and drivingmechanisms, and mechanical structures, and the determination of suitablematerials and structures are within the skill in the art.

The method performed in an automated immunochemistry analysis can alsoinclude the following steps. (a) adjusting the respective cycle of atleast one of the at least two procedures, such that one of the least twoprocedures has an operating cycle of a first period of time and anotherone of the at least two procedures has an operating cycle of a secondperiod of time, and the quotient of the second period of time divided bythe first period of time is a whole number; (b) providing a plurality ofindependent working stations for performing the other one of the atleast two procedures, each working station operating on the cycle of thesecond period of time, such that the number of such stations equal tothe whole number; and (c) staggering apart respective cycles of theindependent working stations by the first period of time, such that atleast one of the working stations is available for each operating cycleof the first period of time.

The analyzer has many unique features and advantages. First, theanalyzer can be capable of having a high throughput, e.g., 400 tests perhour. Second, the analyzer can be capable of providing multiplepipetting modules that can work independently to ensure uninterruptedanalysis, even when one of the modules malfunctions. Third, the analyzercan perform retesting or reflex testing with a large capacity samplestorage area.

FIG. 5A shows a cross-sectional view of an incubation carousel 500according to an embodiment of the invention. FIG. 5B shows across-section of a portion of the incubation carousel 500. FIG. 5C showsa top perspective view of a portion of the incubation carousel 500.

Referring to FIG. 5A, the incubation carousel 500 can include a bodyincluding a top portion 502 in the form of a circular plate with anarray of holes 504 for receiving reaction vessels with samples to beprocessed. Each hole 504 may correspond to a discrete incubation regionwhere a reaction vessel may be subjected to an incubation process. Thetop portion 502 sits on top of a bottom portion 503, which includes anumber of concentric walls 503A (shown in FIG. 5B). The body is situatedon an axis 510 that can cause the incubation carousel 500 to rotate. Ifdesired, heaters such as thin film heating elements may be includedwithin the body so that samples within the holes 504 can be heated ifdesired. The incubator carousel 500 can have other shapes, or more orless holes than are specifically illustrated.

Magnets 508 can be present within the bottom portion 503 of the body ofthe incubation carousel. 500. As shown in FIGS. 5A-5C, the magnets 508are present in the innermost circle of incubation regions, but they partof any suitable number of incubation regions. The magnets may used tobind magnetic particles so that any supernatant that is suitable for adownstream mass spectrometric analysis can be performed. The magnets maybe permanent magnets or electromagnets. An aspiration device (not shown)such as a pipettor may remove any supernatant and may transfer thesupernatant to a sample introduction apparatus, for eventual transfer tothe mass spectrometer.

A wide variety of mass analyzer systems, which can form part of the massspectrometers, can be used in the sample processing system according toembodiments of the invention. Suitable mass analyzer systems include twomass separators with an ion fragmentor disposed in the ion flight pathbetween the two mass separators. Examples of suitable mass separatorsinclude, but are not limited to, quadrupoles, RF multipoles, ion traps,time-of-flight (TOF), and TOF in conjunction with a timed ion selector.Suitable ion fragmentors include, but are not limited to, thoseoperating on the principles of: collision induced dissociation (CID,also referred to as collisionally assisted dissociation (CAD)),photoinduced dissociation (PID), surface induced dissociation (SID),post source decay, by interaction with an electron beam (e.g., electroninduced dissociation (EID), electron capture dissociation (ECD)),interaction with thermal radiation (e.g., thermal/black body infraredradiative dissociation (BIRD)), post source decay, or combinationsthereof.

Examples of suitable mass spectrometers include, but are not limited to,those which comprise one or more of a triple quadrupole, aquadrupole-linear ion trap (e.g., 4000 Q TRAP●LC/MS/MS System, QTRAP●LC/MS/MS System), a quadrupole TOF (e.g., QSTAR●LC/MS/MS System),and a TOF-TOF.

In various embodiments, the mass spectrometer comprises a MALDI ionsource. In various embodiments, at least a portion of the combinedsample is mixed with a MALDI matrix material and subjected toparent-daughter ion transition monitoring using a mass analyzer with aMALDI ionization source.

The mass spectrometer can comprise a triple quadrupole mass spectrometerfor selecting a parent ion and detecting fragment daughter ions thereof.In this embodiment, the first quadrupole selects the parent ion. Thesecond quadrupole is maintained at a sufficiently high pressure andvoltage so that multiple low energy collisions occur causing some of theparent ions to fragment. The third quadrupole is selected to transmitthe selected daughter ion to a detector In various embodiments, a triplequadrupole mass spectrometer can include an ion trap disposed betweenthe ion source and the triple quadrupoles. The ion trap can be set tocollect ions (e.g., all ions, ions with specific m/z ranges, etc.) andafter a fill time, transmit the selected ions to the first quadrupole bypulsing an end electrode to permit the selected ions to exit the iontrap. Desired fill times can be determined, e.g., based on the number ofions, charge density within the ion trap, the time between elution ofdifferent signature peptides, duty cycle, decay rates of excited statespecies or multiply charged ions, or combinations thereof.

One or more of the quadrupoles in a triple quadrupole mass spectrometercan be configurable as a linear ion trap (e.g., by the addition of endelectrodes to provide a substantially elongate cylindrical trappingvolume within the quadrupole). In various embodiments, the firstquadrupole selects the parent ion. The second quadrupole is maintainedat a sufficiently high collision gas pressure and voltage so thatmultiple low energy collisions occur causing some of the parent ions tofragment. The third quadrupole is selected to trap fragment ions and,after a fill time, transmit the selected daughter ion to a detector bypulsing an end electrode to permit the selected daughter ion to exit theion trap. Desired fill times can be determined, e.g., based on thenumber of fragment ions, charge density within the ion trap, the timebetween elution of different signature peptides, duty cycle, decay ratesof excited state species or multiply charged ions, or combinationsthereof.

In some embodiments, the mass spectrometer can comprise two quadrupolemass separators and a TOF mass spectrometer for selecting a parent ionand detecting fragment daughter ions thereof. In various embodiments,the first quadrupole selects the parent ion. The second quadrupole ismaintained at a sufficiently high pressure and voltage so that multiplelow energy collisions occur causing some of the ions to fragment, andthe TOF mass spectrometer selects the daughter ions for detection, e.g.,by monitoring the ions across a mass range which encompasses thedaughter ions of interest and extracted ion chromatograms generated, bydeflecting ions that appear outside of the time window of the selecteddaughter ions away from the detector, by time gating the detector to thearrival time window of the selected daughter ions, or combinationsthereof.

In some embodiments, the mass spectrometer can comprise two TOF massanalyzers and an ion fragmentor (such as, for example, CID or SID). Invarious embodiments, the first TOF selects the parent ion (e.g., bydeflecting ions that appear outside the time window of the selectedparent ions away from the fragmentor) for introduction in the ionfragmentor and the second TOF mass spectrometer selects the daughterions for detection, e.g., by monitoring the ions across a mass rangewhich encompasses the daughter ions of interest and extracted ionchromatograms generated, by deflecting ions that appear outside of thetime window of the selected daughter ions away from the detector, bytime gating the detector to the arrival time window of the selecteddaughter ions, or combinations thereof. The TOF analyzers can be linearor reflecting analyzers.

The mass spectrometer can comprise a tandem MS-MS instrument comprisinga first field-free drift region having a timed ion selector to select aparent ion of interest, a fragmentation chamber (or ion fragmentor) toproduce daughter ions, and a mass separator to transmit selecteddaughter ions for detection. In various embodiments, the timed ionselector comprises a pulsed ion deflector In various embodiments, theion deflector can be used as a pulsed ion deflector. The mass separatorcan include an ion reflector. In various embodiments, the fragmentationchamber is a collision cell designed to cause fragmentation of ions andto delay extraction. In various embodiments, the fragmentation chambercan also serve as a delayed extraction ion source for the analysis ofthe fragment ions by time-of-flight mass spectrometry.

In some embodiments, ionization can be used to produce structurallyspecific fragment ions and Q3 MRM ions. A labeling reagent can be whollyor partly contained in the structurally specific fragment ions. Themethod can provide both sensitivity and specificity for the Q3 MRM ions.In some embodiments, ionization can be used to produce a dominantneutral loss fragment ion which can be selected in Q3 and thenfragmented to produce structurally specific ions. These fragment ionscan then be used for identification and quantification in a procedurereferred to as MS3.

FIG. 6A shows a block diagram of an exemplary mass spectrometer 600 anda sample introduction apparatus 601 coupled to the mass spectrometer. Asample solution may have been transferred from the analyzer, into thesample introduction apparatus 601. The sample introduction apparatus 601can be in the analyzer in some embodiments. The sample introductionapparatus 601 may be coupled to the mass spectrometer 600 through aconnecting tube 602. The sample introduction apparatus 601 may introducethe sample solution to the ion source 603 through the connecting tube602. The ion source 603 can be controlled by an ion source power supply604 through a signal line 605A. Ions concerning sample molecules, whichare generated by the ion source 603, are introduced to a mass analysisregion 606 and mass analyzed. The mass analysis region 606 is evacuatedto a vacuum by a vacuum system 607. The ions thus mass analyzed aredetected by an ion detector 608. A detection signal is fed through asignal line 605B to a data processing unit 609. The data processing unit609 may be a separate unit or may be part of the previously describedcontrol system.

FIG. 6B shows a diagram of a portion of a mass spectrometer using anelectrospray method. FIG. 6B is a sectional view showing the structureof a sample introduction apparatus 619 coupled to an electrospray ionsource. A sample solution provided from the sample introductionapparatus 619 is introduced through a connecting tube 622 and aconnector 630 into a capillary 621 for nebulization. By application of avoltage of the order of kV between the nebulization capillary 621 and acounter electrode 632, small charged droplets of the sample solution areconically nebulized from an end of the nebulization capillary, that is,a so-called electrospray phenomenon occurs. In the electrospray method,an output 623 for nebulizing gas is provided so that gas such asnitrogen gas is poured from the surroundings of the nebulizationcapillary 621 to thereby accelerate the vaporization of the smallcharged droplets. Further, the gas such as nitrogen gas is blown towardthe generated small charged droplets from an outlet 624 for vaporizinggas provided in the counter electrode 632 side to thereby accelerate thevaporization of the small charged droplets. Ions thus generated areintroduced through an ion sampling aperture 625 into a vacuum 626 andmass analyzed by a mass analysis region 626 under a high vacuum.

FIG. 6C shows a structure of an ion detector The structure shown in FIG.6C can be used to improve the signal-to-noise ratio (SIN) in the massspectrometer. An ion deflecting electrode 646 can be provided in therear portion of a mass analysis region 648 for mass separation under ahigh-frequency electric field to deflect mass-separated ions. Thedeflected ions are accelerated at a voltage of the order of kV andcollide with a dynode 657 to produce secondary electrons. Secondaryelectrons are emitted from the secondary electron-producing dynode 657with which the ions collide. The emitted secondary electrons aredetected by an electron detector 658 such as an electron multiplier. Bythe structure shown in FIG. 6C, neutral molecules having no charge,charged droplets or droplets having no charge are prevented from beingdetected as a signal by the ion detector 648, so that improvement in S/Nis attained.

As noted above, a sample introduction apparatus may be disposed betweenthe analyzer and the mass spectrometer. One type of sample introductionapparatus can be a trap and elute apparatus. Details of a suitable trapand alute apparatus can be described with reference to FIGS. 7A and 7B.

FIG. 7A shows a diagram of components in a trap and elute apparatus 700according to an embodiment of the invention in a first configurationFIG. 7B shows the trap and elute system 700 according to an embodimentof the invention in a second configuration.

The trap and elute apparatus 700 includes a first pump 702 and a secondpump 704, which are in fluid communication with a mixer 706. An injector708 is downstream of and in fluid communication with the mixer 706. Theinjector 708 can interface with a series of valves 610. Connectionpoints in the series of valves may be labeled 1-6. The series of valvesmay be present in a switching valve device 710, which may connect to atrap 712, and may connect or disconnect the trap 712 from a downstreamwaste station 718 or a downstream mass spectrometer 720. The trap 712may contain any suitable material such as a C18 material.

In FIG. 7A, a sample to be processed in the mass spectrometer 720 may bepumpted by pump A 702 into the mixer 706, and into the injector 708. Itmay then be injected into the series of valves in the switching valvedevice 710 (the connection points 1-2, 3-4, and 5-6 may be connected)and may flow through the trap and to the waste station. Any analyte ofinterest may be captured in the trap 712, and any liquid component ofthe sample that is not of interest may be transferred to the wastestation 718.

In FIG. 7B, the connection points in the series of valves in theswitching valve device 710 are switched. Now, connection points 2-3,1-6, and 4-5 are connected. As shown, a buffer that is compatible withthe mass spectrometer 720 may be pumped from the second pump 704, to themixer 706, and to the injector 708. The injector 708 may then inject thebuffer to the trap 712 and the buffer will elute any analyte of interestoff of the trap 712 and into the mass spectrometer 720.

The sample processing system may be capable of performing any suitableanalysis on any suitable analyte in any suitable sample. Such analysesmay include immunopurification and detection processes, proteinprecipitation and detection processes, and SISCAPA-type processingmethods. Rather than measure an intact protein directly by massspectrometry, SISCAPA makes use of proteolytic digestion (e.g., with theenzyme trypsin) to cleave sample proteins into smaller peptides ideallysuited to quantitation by mass spectrometry. By selecting a targetpeptide whose sequence occurs only in the selected target protein (aso-called “proteotypic” peptide), the target peptide can serve as adirect quantitative surrogate for the target protein. A syntheticversion of the target peptide containing a stable isotope label canadded in a known amount to the digested sample to serve as an internalstandard (SIS). Since the target peptide and SIS are chemicallyindistinguishable throughout the workflow, but can be measuredseparately by a mass spectrometer due to the mass difference of thestable isotope label, their ratio provides the desired quantitativeestimate of the target peptide amount.

FIGS. 8-10 illustrate processes that utilize the analyzer to prepare asample for a mass spectrometric analysis, and the subsequent massanalysis performed by the mass spectrometer.

FIG. 8 shows a flowchart illustrating an immunopurification processaccording to an embodiment of the invention. Reference can be made withrespect to the analyzer diagram in FIG. 4A above.

In step 802, a sample in a sample tube is loaded into the samplepresentation unit 401 in the analyzer 400. The sample tube may bepresent along with a number of other sample tubes in a sample tube rackor other sample tube carrier.

In step 804, the main sample pipetting station 402 may then pipette oneor more aliquots of the sample in the sample tube into one or morereaction vessels provided by the bulk vessel feeder 403. At this point,the first pick and place gripper 408 may transfer the reaction vessel tothe reagent pipetting stations 404, 405, 406, 407. If two samplealiquots are present in two reaction vessels, then one of the reactionvessels may be transported by the first pick and place gripper 40 to thesample storage 412 for possible future reflex testing or retesting byeither the immunoanalyzer or the mass spectrometer. In some cases, asingle reaction vessel with a sample aliquot may be stored in the samplestorage 412 and may be used for multiple tests (e.g. by taking asecondary aliquot from the reaction vessel and transferring to a thirdvessel). In some cases, 5-10 tests can be run from the initial aliquotin a reaction vessel.

In step 806, in one of the reagent pipetting stations 404, 405, 406,407, magnetic beads coated with an analyte specific capture antibody maybe added to the sample aliquot in the reaction vessel along with anyother suitable reagents. The reagent and the sample aliquot may then bemixed in the reagent pipetting station. Mixing can take place by using apipettor to aspirate and dispense fluid inside of a reaction vesselrepeatedly or by any other suitable mixing process. Note also that eventhough reagents are described as being pipetted in this and otherexamples, it is understood that reagents may be added to reactionvessels in any suitable manner. For example, dry reagents may be presentor added to reaction vessels before or after sample aliquots are addedto them.

After the appropriate reagents are added to the reaction vesselcontaining the sample aliquot, the second pick and place gripper 409 maytransfer the reaction vessel to the incubator/wash/read station 412.

In step 808, in the incubator in the incubator/wash/read station 412,the reaction vessel containing the magnetic beads and the sample may beincubated to capture any analyte of interest on the antibodies attachedto magnetic particles. The mixture in the reaction vessel may beincubated for any suitable amount of time (e.g., 60 minutes).

In step 810, in the wash apparatus in the incubator/wash/read station412, the magnetic beads may be washed with a wash fluid, andmagnetically separated from the supernatant. A pipettor in the washapparatus can be used to dispense and remove any fluid from the reactionvessel to perform this process.

Once the washing process is completed, the second pick and place gripper409 may then transport the reaction vessel to the reagent pipettingstations 404, 405, 406, 407. Once the analyte of interest is bound tothe antibodies on the magnetic particles, the control system candetermine if an immunoassay detection process or a mass spectrometricanalysis process is to be performed. In some cases, the determination asto whether an immunoassay detection process or a mass spectrometricanalysis process is to be performed can be made earlier in the process.

If an immunoassay detection process is to be performed, then one of thepipetting stations 404, 406, 406, 407 may dispense a chemiluminescentsubstrate or other optical substrate into the reaction vessel.Alternatively, the substrate can be added to the reaction vessel by adedicated pipettor in the washing system. The reaction vessel may thenbe transferred by the second pick and place gripper 409 to the incubatorin the incubator/wash/read station 412. In the incubator, thechemiluminescent substrate may bind to the analyte of interest, stillbound to the magnetic beads. The reaction vessel may then be transferredfrom the incubator to the reader in the incubator/wash/read station 412using the third pick and place gripper 410. The reader may then detectif analyte is present and/or the concentration of the analyte.

In some embodiments of the invention, the detection process may beperformed by a mass spectrometer. Steps 812, 814, 816, 822, 824, 826,and 828 can be performed when a mass spectrometer is used to detect thepresence or concentration of the analyte in the sample.

In step 812, instead of adding one or more optical detection reagents(e.g., a chemiluminescent subtract) into the reaction vessel, one of thereagent pipetting stations 404, 405, 406, 407 may add an elution bufferto the reaction vessel containing the processed sample. The reagentpipetting station may then mix the elution buffer with the magneticparticles including the bound analyte. After this step has beenperformed, the second pick and place gripper 409 may then transfer thereaction vessel to the incubator in the incubator/wash/read station 412.

In step 814, in the incubator, an incubation process may be performed inthe incubator in the incubator/wash/read station 412. The mixture in thereaction vessel may be incubated for any suitable period of time.

In step 816, a magnetic separation process can be performed in a washstation in the incubator/wash/read station 412 to separate thesupernatant from the magnetic particles. Alternatively, as noted above,a magnetic separation process can be performed in the incubator in theincubator/wash/read station 412 if the incubator includes incubationregions with magnets. In other case, a magnet in either the wash stationor the incubator in the incubator/wash/read station 412, or even in oneof the pipetting stations 404, 405, 406, 407 may allow confine themagnetic particles to a location in the reaction vessel.

In step S822, the supernatant containing the analyte of interest in thereaction vessel may be transferred to a second reaction vessel usingpipettor proximate to the incubator/wash/read station, or at any othersuitable location, leaving behind the magnetic particles in the firstreaction vessel.

In step 824, the second reaction vessel or the supernatant containingthe analyte of interest may be transferred to the mass spectrometerusing one or more of sample introduction apparatuses.

If desired, at this point in the process, one or more mass tags orderivatizing agents may be added to the supernatant containing theanalyte of interest. The mass tags or derivatizing agent can be added byone of more of the reagent pipetting stations 404, 405, 406, 407.

In step 826, once the supernatant containing the analyte of interest isin the mass spectrometer, a mass analysis can be performed.

In step 828, a data analysis may be performed by the mass spectrometer,as described above.

FIG. 9 shows a flowchart illustrating a protein precipitation processaccording to an embodiment of the invention. In a protein precipitationprocess, proteins in a sample that are not of interest can be bound tomagnetic particles. The magnetic particles may be separated from asupernatant containing the analyte of interest in a reaction vessel. Theanalysis illustrated in FIG. 9 can be performed instead of animmunoassay process or as a reflex test for a prior immunoassay process.

In step 902, a sample in a sample tube is loaded into the samplepresentation unit 401 in the analyzer 400. The sample tube may bepresent along with a number of other sample tubes in a sample tube rackor other sample tube carrier.

In step 904, the main sample pipetting station 402 may then pipette amixture of an aliquot of the sample, assay standard, and precipitationbuffer containing paramagnetic microparticles into the reaction vesselprovided by the bulk vessel feeder 403. The mixture in the reactionvessel may then be mixed at the main sample pipetting station usingmultiple dispense and aspiration steps, or using any other suitablemixing process.

At this point, the second pick and place gripper 409 may transfer thereaction vessel to the incubator/wash/read station 412.

In step 906, in the incubator in the incubator/wash/read station 412,the reaction vessel containing the mixture may be incubated, so that anyprotein matrix within the sample aliquot is bound to the paramagneticmicroparticles.

In step 908, in the wash apparatus in the incubator/wash/read station412, the paramagnetic microparticles with the bound protein matrixmagnetically separated from the supernatant containing the analyste ofinterest. Alternatively, as noted above, a magnetic separation processcan be performed in the incubator in the incubator/wash/read station 412if the incubator includes incubation regions with magnets.

In step 910, the supernatant containing the analyte of interest in thereaction vessel may be transferred to a second reaction vessel providedby the bulk vessel feeder 403 using a pipettor proximate to theincubator/wash/read station 412.

In step 914, once the supernatant containing the analyte of interest isin the mass spectrometer, a mass analysis can be performed.

In step 916, a data analysis may be performed by the mass spectrometer.

In some embodiments, instead of performing steps 908, 910, and 912, theanalyzer could transfer the reaction vessel to a centrifuge module(which may be located in the analyzer, the mass spectrometer, or may beseparate from them), spun, and then returned to the analyzer.

FIG. 10 shows a flowchart illustrating another immunopurificationprocess according to an embodiment of the invention. The processillustrated in FIG. 10 may be a SISCAPA-type processing method asdescribed above.

In step 1002, a sample in a sample tube is loaded into the samplepresentation unit 401 in the analyzer 400. The sample tube may bepresent along with a number of other sample tubes in a sample tube rackor other sample tube carrier.

In step 1004, the main sample pipetting station 402 may then pipette analiquot of the sample in the sample tube, and a denaturingreagent/alkenylating reagent, into a reaction vessel provided by thebulk vessel feeder 403. The first pick and place gripper 408 may thentransfer the reaction vessel to the incubator in the incubator/wash/readstation 412 so that an incubation process can be performed.

In step 1006, the reaction vessel containing the sample is incubated.

After incubation, the second pick and place gripper 409 may transfer thereaction vessel to the reagent pipetting stations 404, 405, 406, 407.

In step 1008, one of the reagent pipetting stations 404, 405, 406, 407may add trypsin and may mix the resulting mixture in the reactionvessel. The second pick and place gripper 409 may then transfer thereaction vessel to the incubator in the incubator/wash/read station 412.

In step 1010, in the incubator, an incubation process may be performedin the incubator of the incubator/wash/read station 412. At this point,the second pick and place gripper 409 may transfer the reaction vesselto one of the reagent pipetting stations 404, 405, 406, 407.

In step 1012, one of the reagent pipetting stations 404, 405, 406, 407may add magnetic microparticles coated with antibodies and SIS peptides.After this step has been performed, the second pick and place gripper409 may then transfer the reaction vessel to the incubator in theincubator/wash/read station 412.

In step 1014, in the wash apparatus in the incubator/wash/read station412, a magnetic separation and wash process may be performed. Once thisprocess step has been performed, the second pick and place gripper 409may then transport the reaction vessel to the reagent pipetting stations404, 405, 406, 407.

In step 1016, one of the reagent pipetting stations 404, 405, 406, 407may add an elution buffer and may then mix the elution buffer with themagnetic particles including the bound analyte. After this step has beenperformed, the second pick and place gripper 409 may then transfer thereaction vessel to the incubator in the incubator/wash/read station 412.

In step 1018, in the incubator, an incubation process may be performedin the incubator in the incubator/wash/read station 412.

In step 1020, a magnetic separation process can be performed in a washstation in the incubator/wash/read station 412. Alternatively, as notedabove, a magnetic separation process can be performed in the incubatorin the incubator/wash/read station 412 if the incubator includesincubation regions with magnets.

In step 1022, the supernatant containing the analyte of interest in thereaction vessel may be transferred to a second reaction vessel usingpipettor proximate to the incubator/wash/read station.

In step 1024, the second reaction vessel or the supernatant containingthe analyte of interest may be transferred to the mass spectrometerusing one or more sample introduction apparatuses.

In step 1026, once the supernatant containing the analyte of interest isin the mass spectrometer, a mass analysis can be performed.

In step 1028, a data analysis may be performed by the mass spectrometer.

The sample processing systems and methods disclosed herein can be usedto improve the quality and efficiency of a variety of tests to benefitpatients. The following are non-limiting examples.

Drugs of Abuse

In some embodiments, the sample processing system can be used to processa biological sample according to a test order to detect one or moredrugs of abuse in a patient. The drug of abuse may be one that isselected from the group consisting of: alcohol, amphetamines,benzoylecgonine, opiates, barbiturates, morphine, benzodiazepines,cocaine, marijuana, methadone, methamphetamines, tetrahydrocannabinol,hydrocodone, hydromorphone, oxycodone, codeine, 6-monoacetylmorphine,meperidine, phencyclidine propoxyphene, oxymorphone, fentanyl, andphencyclidine (PCP).

Bodily fluid samples can be collected from the patient for the test.Suitable examples of bodily fluid include, but not limited to, blood,saliva, sweat, and urine. The samples can then be prepared, andappropriate analyzer(s) can be determined using the above-describedcondition sets and parameters. For example, a condition set maydetermine that a particular biological sample is to be analyzed using amass spectrometer. The biological sample is then prepared according to astandard mass spectrometry sample preparation procedure. Preparedsamples can then be introduced into a mass spectrometer and the amountsof each of the one or more drugs of abuse and their metabolites can bemeasured. Each of the measurements can be compared with a predeterminedreference range, which corresponds to the levels of the drug inindividuals who do not abuse,—if the measurement is greater than theupper limit of the respective reference, the patient is determined tohave abused the drug. Optionally, the system may generate a report ofpatient compliance or abuse based on the comparison. In a more specificexample, for drugs of abuse, an order could be to test for a drug ofabuse such as an opioid. Since the clinical value can be extremelylow—the system would then the suggest using a mass spectrometer

Therapeutic Drug Monitoring

In some embodiments, the sample processing system can be used to processa biological sample according to a test order to monitor a patient'scompliance with his or her prescription of a therapeutic drug. Typicallythe patient's prescription record is stored in the patent information inthe information management apparatus, which may including an HIS or LIS.A bodily fluid sample can be periodically collected from the patient whois taking a prescription drug and analyzed using a mass spectrometer orother analyzer. The specific analyzers may be selected based upon theabove described test order, condition sets, and parameters. The drug orthe metabolites thereof in each of the samples can be detected,quantified, and compared with the patient's prescription record tomonitor whether the patient is take the prescribed drug in theprescribed amounts. For example, a detected amount that is above theupper limit of the reference range indicates that the patient has beenoverdosed and a detected amount that is below the lower limit of thereference range indicates that the patient has not taken the drug insufficient amount and/or frequency.

One particular category of therapeutic drugs is immunosuppressant drugs,which are typically given to organ transplant patients to preventtransplant rejection. Immunosuppressant drugs require close monitoringbecause of their narrow therapeutic index and significantinter-individual variability in blood concentrations. This variabilityis typically due to factors such as drug-nutrient interactions,drug-disease interactions, renal-insufficiency, inflammation andinfection, gender, age, polymorphism and liver mass. Suitableimmunosuppressant drugs can be measured using the sample processingsystem of the invention include, but are not limited to, cyclosporine,tacrolimus, sirolimus and mycophenolic acid. In some cases, the methodfurther comprises comparing the measurement value with a reference rangethat is deemed to be safe for organ transplant and determining organtransplant can be performed if the measurement value is within apredetermined reference range, or determining that additional amount ofthe immunosuppressant needs to be administered if the measurement valuesare lower than the lower limit of the reference range.

Steroids

In some embodiments, the sample processing system can be used to processa biological sample according to a test order to determine whether ornot a biological sample of a patient contains steroids at a particularconcentration. For example, one may wish to determine if a patient ispregnant. This typically involves testing pregnancy-related hormones,such as luteinizing hormone (LH) and human chorionic gonadotropin (hCG).

In a female, LH secretion induces ovulation of mature follicles andleads to secretion of estradiol and progesterone, which is necessary formaintenance of pregnancy. HCG is typically produced 6-7 days afterfertilization occurs and continues to rise during pregnancy and can beused to determine the stage of the pregnancy. Thus, the hCG levels inblood and comparison with a reference value can be used to determinepregnancy status. In some cases, the testing of the pregnancy-relatedhormones can be assayed simultaneously with the Down syndrome panel, asdescribed below. In some cases, the testing of pregnancy could beassayed simultaneously with other tests if the age of the mother wasabove a threshold—for example, if the mother is older than 35. Thesystem could also analyze the sample for Down's syndrome (for exampleusing a Molecular Biology analyzer). Or if the mother has a history ofhaving taken a drug known to cause birth defects, the sample could besimilarly be tested.

In some embodiments, the system and methods disclosed herein can be usedto determine whether the fetus has Down syndrome by assaying a panel ofanalytes. The Down syndrome panel of analytes typically includealpha-fetoprotein (AFP), estriol, human chorionic gonadotropin, inhibinA, and pregnancy-associated plasma protein-A (PAPP-A). When the fetushas Down syndrome, the AFP and estriol levels are decreased, while thebeta unit of the hCG and inhibin A are increased in blood. The Downsyndrome panel is typically determined during the second trimester ofpregnancy. Thus, the disclosure provides a system to determine thewhether the fetus has Down syndrome by obtaining a blood sample from thepatient and assaying the amount of analytes including alpha-fetoprotein(AFP), estriol, human chorionic gonadotropin, inhibin A, andpregnancy-associated plasma protein-A (PAPP-A) using the systemdescribed above. A detection of inhibin A and a beta unit of the humanchorionic gonadotropin levels above respective reference levels, and adetection of AFP and estriol levels below their respective referencelevels indicate the fetus has Down's syndrome.

The various analyzers in the sample processing system can be used totest for the presence of steroids in a biological sample. The specificanalyzers may be selected based upon the above described test order,condition sets, and parameters.

Vitamin D

In some embodiments, the sample processing system can be used to processa biological sample according to a test order to detect vitamin D in thebiological sample. Monitoring a vitamin D amount in body is desirable:on one hand, vitamin D deficiencies can have devastating consequences onbone development, immune function and cancer prevention, on the otherhand, vitamin D toxicity resulting from over medication can causehypercalcemia, which is often accompanied with symptoms of stomachupset, nausea, vomiting and constipation. Hypercalcemia can also weakenthe bones and create kidney stones.

Vitamin D has two bioequivalent forms: vitamin D2, which are obtainedfrom vegetable sources, and vitamin D3, which are derived fromendogenous sources (synthesized from cholesterol through sun exposure)and exogenous sources (animal diet). Vitamin D exists in the body mainlyin the form of 25-hydroxyvitamin D and thus the amount of25-hydroxyvitamin D corresponds to the amount of vitamin D the bodystores. The total amount of 25-hydroxyvitamin D is the sum of25-hydroxyvitamin D2 and 25-hydroxyvitamin D3. In some cases,25-hydroxyvitamin D2 and 25-hydroxyvitamin D3 levels are also separatelyassessed, which allows identification of the source of the deficiencyand prescribing treatment. For example, a low level of 25-hydroxyvitaminD2 may indicate that the patient would benefit from increasing vegetableintake.

The reference value for vitamin D, i.e., normal amount of vitamin D istypically within the range of 25-80 ng/mL. A detection of an amount thatis lower than 25 ng/mL thus may indicate vitamin D deficiency and anamount that is higher than 80 ng/mL may indicate the excessive vitaminD. Physicians can prescribe treatment accordingly based on theinformation.

The various analyzers in the sample processing system can be used totest for the presence of vitamin D in a biological sample. The specificanalyzers may be selected based upon the above described test order,condition sets, and parameters.

Sepsis

In some embodiments, the sample processing system can be used to processa biological sample according to a test order to diagnose sepsis. Sepsisdevelops when the immune system releases certain chemicals into thebloodstream to fight an infection, which cause inflammation throughoutthe entire body. Severe cases of sepsis can lead to septic shock, alife-threatening condition. Detection of sepsis provides cliniciansvaluable information to determine whether antibiotics should beimmediately administered in certain situations when the patient isespecially vulnerable for infection, such as during or after surgerySepsis is typically diagnosed based on one or more of the analytesselected from the group consisting of C-reactive protein (CRP),interleukin-6 (IL-6), and procalcitonin. Normal CRP ranges in blood maybe less than 10 mg/l; levels of 10 to 50 mg/l indicate an infection withlow or medium impact likely caused by a local infection; and levels of50 to 100 mg/l indicate a high infection with a root cause analysis andimmediate attention required. In addition, IL-6 activates increasingleucocyte population in the blood count and can forewarn of an upcominginfection even before the fever of the patient is detected by theclinician. The test results of the IL-6 and procalcitonin tests areuseful to distinguish between a bacterial infection and an autoimmunereaction due to a chronic disease—in the case of a bacterialinflammation the procalcitonin value increases, while in the case of aviral infection the procalcitonin value is mostly in the normal range.Thus, a comparison of the measurements of these markers with respectivereference ranges can be used to diagnose sepsis and also to identify thesource of infection, thus allowing clinicians to provide propertreatment to the patient.

The various analyzers in the sample processing system can be used totest for the presence of analytes that may be indicative of sepsis in abiological sample. The specific analyzers may be selected based upon theabove described test order, condition sets, and parameters.

For sepsis, in some embodiments, a MDW score on a hematology unit wouldresult in the system using an immunoassay analyzer (IA) or MS (massspectrometer) to test for PCT, IL6, IL8 levels—or directing sample to becultured and then tested on a microbiology system. Or, one could firsttest for high PCT, and then send to the hematology unit for the MDWscore. Another case would be that where a patient has recently hadsurgery; if the clinician notes inflammation—then test for PCT and MDWto rule out sepsis.

Alzheimer's Disease

In some embodiments, the sample processing system can be used to processa biological sample according to a test order to diagnose Alzheimer'sdisease. Tests can be typically performed on cerebrospinal fluid (CSF),plasma, saliva, or whole blood samples collected from the patient toanalyze one or more protein/steroid markers such as phosphorylated-Tauprotein, total Tau protein, CSF amyloid beta (1-42), C-reactiveproteins, homocysteine, alpha-sunuclein, neuron-specific enolase (NSE),and dehydroepiandrosterone sulphate. A patient having Alzheimer'sdisease typically has increased amounts in one or more of theaforementioned markers as compared to controls. In some cases, adecrease in circulating miRNAs, such as miR-125b, miR-23a, and miR-26b,and/or an increase in the amount of reactive oxygen species (ROS) canalso be used to diagnose Alzheimer's disease. See Galimberti et al.,Circulating miRNAs as potential biomarkers in Alzheimer's disease, J.Alzheimer's Dis. 2014; 42(4): 1261-7.; Huang et al. Role of oxidativestress in Alzheimer's disease, Biomed. Rep. 2016 May; 4(5): 519-522.

Thus, the disclosure provides sample processing systems and methods fordetermining whether a patient has Alzheimer's disease by obtaining abodily fluid sample, such as cerebrospinal fluid (CSF), plasma, saliva,or whole blood, from the patient, and assaying the amount of one or moreof the following analytes: phosphorylated-Tau protein, total Tauprotein, CSF amyloid beta (1-42), C-reactive proteins, homocysteine,alpha-sunuclein, neuron-specific enolase (NSE), anddehydroepiandrosterone sulphate, miR-125b, miR-23a, and miR-26b, andROS. The results may be compared with reference values stored in thecontrol system and a diagnosis can be made based on the comparison asdescribed above.

The various analyzers in the sample processing system can be used totest for the presence of analytes that may be indicative of Alzheimer'sdisease in a biological sample. The specific analyzers may be selectedbased upon the above described test order, condition sets, andparameters.

Cardiac Disease and Stroke

In some embodiments, the sample processing system can be used to processa biological sample according to a test order to detect the risk ofhaving cardiac disease or a stroke. Many forms of cardiovasculardiseases begin with atherosclerosis, a condition where the arteriesbecome hardened and narrowed due to plaque build-up around the arterywall. Plaque—made of cholesterol, fatty substances, cellular wasteproducts, calcium and fibrin—may partially or totally block the blood'sflow through an artery in the heart, brain, pelvis, legs, arms orkidneys. This blockage may develop into serious diseases, such ascoronary heart disease, chest pain, carotid artery disease, peripheralartery disease (PAD) and chronic kidney disease. Even worse, if a pieceof the plaques breaks off or a blood clot (thrombus) forms on theplaque's surface, a heart attack or stroke may result.

A number of lipoprotein markers are good biomarkers for cardiac diseaseand can be measured from bodily fluid samples collected from thepatient, e.g., blood, plasma, serum using the mass spectrometer. Thesemarkers include B-type natriuretic peptide (BNP), proBNP (a non-activeprohormone that produces BNP), human C-reactive protein (hs-CRP) andpregnancy associated plasma protein-A (PAPP-A). Many of thesenatriuretic peptides can aid in determination of plaque progression andrisk of onset of stroke. Other markers include triglyceride to HDLp(high density lipoproteins) ratio, lipophorin-cholesterol ratio,lipid-lipophorin ratio, LDL cholesterol level, HDLp and apolipoproteinlevels, lipophorins and LTPs ratio, sphingolipids, Omega-3 Index, andST2 levels, which can be assayed using the mass spectrometer of thesystem. The measurements can be compared with reference ranges accordingto pre-stablished rules to determine the risk of cardiac disease orstroke.

The various analyzers in the sample processing system can be used totest for the presence of analytes that may be indicative of cardiacdisease and/or stroke in a biological sample. The specific analyzers maybe selected based upon the above described test order, condition sets,and parameters.

Cancer

The present sample processing system can also be used to detect variouscancers. Cancer typically refers to the physiological condition inmammals that is typically characterized by unregulated cell growthand/or proliferation. Patients who developed particular cancers may shownotable differences in levels of cancer-specific markers, in blood,serum, plasma or other bodily fluid as compared to healthy individuals.However, as with other tests, a single marker on its own often is notspecific or sensitive enough to diagnose cancers, especially those thatare still in early stages. The systems and methods disclosed herein areespecially advantageous in that they can be utilized to test a panel ofbiomarkers, which collectively, can be used to detect the presence ofthe cancer with high accuracy. The cancer-specific biomarkers mayinclude protein markers and DNA markers. In some cases, the proteinmarkers detection is combined with DNA markers detection method tofurther increase the assay sensitivity and specificity. The samples canbe analyzed using a mass spectrometer in the system to detect and/orquantifying the amount of the protein markers. In some cases, thesamples are further analyzed using an immunoanalyzer to confirm theidentity of the protein markers. In other cases, the samples are furtheranalyzed using a molecular biology analyzer of the system to furtherassess the DNA markers. The measurements of these cancer-specificmarkers can be compared with reference ranges according topre-stablished rules to detect the presence of and/or stage of cancer. Afew specific cancers are discuss below as illustrative examples.

In some embodiments, the sample processing system can be used to processan test order for detecting breast cancer. In general, relative tohealthy individuals, breast cancer patients have a higher averageconcentration of insulin-like growth factor-1 (IGF-1), IGF-2,IGF-binding protein 2 (IBP2), IBP3 and leucine-rich a-2-glycoprotein(A2GL), Erbb2/HER2, osteopontin, enolase 1 (ENO1), PKM2 and LDHA and/orfibulin-2. Thus detecting an increase in one or more of these markersmay indicate the patient has breast cancer. Once diagnosed with breastcancer, the subject can also be periodically tested for the plasmalevels of fibronectin, clusterin, gelsolin and a-1microglobulin/inter-a-trypsin inhibitor light chain precursor (AMBP), anincrease of one or more of these markers generally indicates anadvancement of the breast cancer.

In some embodiments, the sample processing system can be used to processan test order for detecting colorectal cancer. In colorectal cancerpatients, ademosylhomocysteinase (AHCY), cathepsin D (CTSD), S100A9 andlysozyme C (LYZ) are increased relative to healthy individuals and theamount of these markers in colorectal cancer blood samples across thefour stages of colorectal cancer are known. In addition, collagen a-1(I) chain (COL1A1) and maltase-glucoamylase (MGAM) are decreased andinter-a trypsin inhibitor heavy chain H3 (ITIH3) and coagulation factorV (F5) are increased relative to controls. The mass spectrometer of thesystem can be used to detect one or more the markers above and resultcan be used to diagnose colorectal cancer. Advantageously, a massspectrometer can detect differences in structural sugar compositions;this is crucial for diagnosis of invasive and metastatic colon cancer asaberrant glycoforms of both tissue inhibitor of metalloproteinase 1(TIMP1) and protein tyrosine phosphatase k (PTPk) are typically higherthan the patients who do not have these aggressive forms of coloncancers.

In some embodiments, the sample processing system can be used to processan test order for detecting prostate cancer. In prostate cancerpatients, PSA and its post-translationally modified forms along with thesialylated forms of PSA are increased as compared to healthyindividuals. In addition, the presence of N-acylethanolamine acidamidase and protein tyrosine kinase 7 has been shown to be significantlyassociated with aggressive prostate cancer. Further vinculin andgalectin-3 have been shown to be urinary biomarkers for recurrentprostate cancer. Thus, the system can be used to detect prostate cancerby assaying one or more of the markers above to diagnose prostatecancer.

In some embodiments, the sample processing system can be used to processan test order for detecting ovarian cancer. In ovarian cancer patients,a panel of analytes comprising CLIC1, CLIC4, TPM1, TPM2, TPM3, TPM4, andinhibin have been shown to be significantly up-regulated in ovariancancer in comparison to healthy controls and thus one or more of theabove markers can be detected using the analyzers of the system. Inpreferred embodiments, the panel to be tested comprise all sixaforementioned analytes. In some cases, the panel of analytes to betested can further include CA 125. In addition, the system and methoddisclosed herein can also be used to distinguish benign ovarian tumorsversus malign ovarian tumors by testing panels of beta-2-microglobulin,ApoA1, transthyretin and transferrin—these analytes show significantincrease in serum samples in subjects with benign ovarian tumors ascompared to patients having malign ovarian tumors.

In some embodiments, the sample processing system can be used to processan test order for detecting lung cancer. Lung cancer is one of the mostcommon cancer diseases with very poor prognosis and high mortality. Anumber of biomarkers have been reported to associate with lung cancer,such as CEA, AGP, neuron-specific enolase (NEA), however thesebiomarkers lack the desired sensitivity and specificity. Recently, othermarkers such as sialyated (SAA) isoforms SAA1 and SAA2, haptoglobin (Hp)subunits (mostly a chain), a-1B-glycoprotein (A1BG) and leucine-richa-2-glycoprotein (LRG1), are shown to be elevated in sera from lungcancer patients as compared to controls. Other useful markers that canbe detected are zyxin and CD109, the up-regulation of which indicatelung cancer progression and toward metastatic late stage. Thus, in someembodiments, the present system is used to detect and/or measure one ormore biomarkers selected from the group consisting of are sialyated(SAA) isoforms SAA1 and SAA2 levels, haptoglobin (Hp) subunits (mostly achain), a-1B-glycoprotein (AIBG) and leucine-rich a-2-glycoprotein(LRG1), zyxin, and CD109. The measurements can then be compared withrespective reference values to determining the presence and the stage oflung cancer according established correlations between the amounts ofthese markers and status of the disease.

In some embodiments, the sample processing system can be used to processan test order for detecting pancreatic cancer. Pancreatic cancer is thefourth leading cause of cancer-related death in the United States CA19-9is one of the markers who have been found to be upregulated and suchupregulation can be detected in blood samples of the patients. However,in some cases detection of CA19-9 sensitivity is low and detection ofadditional biomarkers such as a-fibrinogen-containing hydroxylatedproline and serotransferin peptide in bodily fluid sample, such as bloodor serum, are necessary to improve assay accuracy. The levels of thesemarkers are typically increased in patients bearing pancreatic cancer incomparison with healthy controls. In addition, an increase in the levelsof transforming growth factor beta-induced (TGFBI), later transforminggrowth factor beta binding 2 (LTBP2) and/or asporin (ASP) as compared tocontrols can be used to diagnose pancreatic ductal adenocarcinoma(PDAC).

In some embodiments, the sample processing system can be used to processan test order for detecting bladder cancer. Bladder cancer is the mostcommon carcinoma of the urinary tract. Biomarkers including the CD44antigen, clusterin, adiponectin, afamin, ApoA-II precursor, CERU,complement C4 gamma chain and prothrombin; measuring one or more ofthese markers in suitable bodily fluid samples may be used to diagnosebladder cancer.

Hepatocellular cancer is the second leading cause of cancer-relateddeath worldwide due to latent liver disease and late diagnosis. A numberof N-glycoproteins, such as AGP, CERU, a-HS-glycoprotein, kininogen-1and carboxypeptidase B2, are increased more than 2.5-fold in livercancer patients relative to controls. Other markers include APF, actinbinding-protein aniline (ANLN), filamin B (FLNB) and complementary C4-A(C4A). Thus, in some cases, the system is configured to measure thelevels of one or more biomarkers selected from the group consisting ofAGP, CERU, a-HS-glycoprotein, kininogen-1 and carboxypeptidase B2, APF,ANLN, FLNB, and C4A, and measurements of one or more of these biomarkersto determine the presence of hepatocellular cancer.

In addition the aforementioned types of cancer, other types of cancercan be similarly diagnosed by measuring biomarkers that are specific tothat cancer using the systems and methods disclosed herein. Non-limitingexamples of the types of cancer include, carcinoma, lymphoma (e.g.,Hodgkin's and non-Hodgkin's lymphoma), blastoma, sarcoma, and leukemia.More particular examples of such cancers can include squamous cellcancer, small-cell lung cancer, non-small cell lung cancer,adenocarcinoma of the lung, squamous carcinoma of the lung, cancer ofthe peritoneum, gastrointestinal cancer, pancreatic cancer,glioblastoma, cervical cancer, liver cancer, bladder cancer, hepatoma,cancer, endometrial or uterine carcinoma, salivary gland carcinoma,kidney cancer, liver cancer, prostate cancer, vulval cancer, thyroidcancer, hepatic carcinoma, leukemia and other lymphoproliferativedisorders, and various types of head and neck cancer.

The various analyzers in the sample processing system can be used totest for the presence of analytes that may be indicative of cancer in abiological sample. The specific analyzers may be selected based upon theabove described test order, condition sets, and parameters.

The above description is illustrative and is not restrictive. Manyvariations of the invention will become apparent to those skilled in theart upon review of the disclosure. The scope of the invention should,therefore, be determined not with reference to the above description,but instead should be determined with reference to the pending claimsalong with their full scope or equivalents.

One or more features from any embodiment may be combined with one ormore features of any other embodiment without departing from the scopeof the invention.

A recitation of “a”, “an” or “the” is intended to mean “one or more”unless specifically indicated to the contrary.

All patents, patent applications, publications, and descriptionsmentioned above are herein incorporated by reference in their entirety.

1-40. (canceled)
 41. A method performed by a system comprising aplurality of analyzers comprising a mass spectrometer and animmunoanalyzer, a sample introduction apparatus, and a control system,the control system operatively coupled to the mass spectrometer, theimmunoanalyzer, and the sample introduction apparatus, the methodcomprising: determining, by the control system, that a massspectrometric analysis is to be performed; transferring to a firstreaction vessel, by the sample introduction apparatus, a sample aliquot;performing, by the immunoanalyzer, separation of an analyte in thesample aliquot in the first reaction vessel to produce a separatedanalyte; transferring the separated analyte to a second reaction vessel;transferring, by the sample introduction apparatus, the second reactionvessel to the mass spectrometer; and performing, by the massspectrometer, an analysis of the analyte.
 42. The method of claim 41,wherein the system further comprises a data processor and a computerreadable medium, the computer readable medium comprising code,executable by the data processor to determine that the massspectrometric analysis is to be performed.
 43. The method of claim 41,wherein the system further comprises an information managementapparatus, the method further comprising receiving, by the informationmanagement apparatus, from the mass spectrometer, one or moremeasurement values for the analyte.
 44. The method of claim 43, whereina test order is communicated to the information management apparatus andcauses the control system to determine that a mass spectrometricanalysis is to be performed.
 45. The method of claim 41, wherein thecontrol system directs a mass tag to be added to the sample aliquot. 46.The method of claim 41, wherein the control system directs an internalstandard of the analyte to be added to the sample aliquot prior to amass spectrometric analysis.
 47. The method of claim 41, wherein thesample aliquot is from a patient.
 48. The method of claim 47, whereinthe mass spectrometric analysis generates at least one value for theanalyte and, the method further comprises comparing, by the informationmanagement apparatus, the at least one value for the analyte withpatient information in a patient repository.
 49. The method of claim 48,wherein the method further generates an output after the comparison. 50.The method of claim 41, wherein the sample aliquot is a biologicalsample.
 51. The method of claim 50, wherein the biological sample isselected from the group consisting of blood, plasma, serum, bodilyfluids, excretions, saliva, urine, cerebrospinal fluid, lacrimal fluid,perspiration, gastrointestinal fluid, amniotic fluid, mucosal fluid,pleural fluid, and sebaceous oil.
 52. The method of claim 41, whereinthe analyte is selected from the group consisting of organic molecules,hormones, metabolites, proteins, lipids, carbohydrates, sugars,steroids, peptides, nucleic acid segments, biomarkers, drugs, moleculeswith a regulatory effect in enzymatic processes such as promoters,activators, inhibitors, or cofactors, microorganisms, fungus, parasites,cells, cell components, spores, and nucleic acids.
 53. The method ofclaim 52, wherein a test order is communicated to an informationmanagement apparatus to test for at least one drug or metabolite thereofor both, and the control system determines that a mass spectrometricanalysis is to be performed.
 54. The method of claim 41, wherein thesample introduction apparatus comprises universal trap columns andsolvents.
 55. The method of claim 41, wherein the separation is magneticseparation.
 56. The method of claim 41, wherein the separation isimmunoprecipitation.
 57. The method of claim 41, wherein the sampleintroduction apparatus is physically and/or operationally coupled to theimmunoanalyzer and/or mass spectrometer.
 58. The method of claim 41,wherein the plurality of analyzers further comprises a hematologyanalyzer, a microbiology analyzer, a chemistry analyzer, a urineanalyzer, a biochemical analyzer, and/or a molecular biology analyzer.59. The method of claim 41, wherein the plurality of analyzers arepresent in one housing.
 60. The method of claim 43, wherein theinformation management apparatus and the plurality of analyzers arepresent in one housing.
 61. A system comprising a plurality of analyzerscomprising a mass spectrometer and an immunoanalyzer, a sampleintroduction apparatus, and a control system, the control systemoperatively coupled to the mass spectrometer, the immunoanalyzer, andthe sample introduction apparatus, wherein: the control system isconfigured to determine that a mass spectrometric analysis is to beperformed and the sample introduction apparatus is configured totransfer a sample aliquot to a first reaction vessel, a second reactionvessel, and/or a mass spectrometer.